i

SURFACE WATER QUALITY MONITORING PROGRAM.................................................................. 6

METHODOLOGY.................................................................................................................................. 23

STATEWIDE SURFACE WATER QUALITY SUMMARY.................................................................. 30

LAKE WATER QUALITY ASSESSMENT............................................................................................ 37

RIVER BASIN WATER QUALITY ASSESSMENTS............................................................................ 42

WETLANDS......................................................................................................................................... 157

PUBLIC HEALTH/AQUATIC LIFE CONCERNS............................................................................... 160

POINT SOURCE POLLUTION CONTROL PROGRAM..................................................................... 169

NONPOINT SOURCE POLLUTION CONTROL PROGRAM............................................................ 171

APPENDIX A – WATERBODIES WITH EPA APPROVED TMDLS ................................................ 184

APPENDIX B – SD DENR 2008 WATERBODY DELISTING REPORT............................................ 187

APPENDIX C – SURFACE WATER QUALITY MONITORING SCHEDULE AND...............................

SAMPLING SITE DESCRIPTION........................................................................................................ 193

APPENDIX D – MEDIAN TSI SECCHI-CHLOROPHYLL FOR ASSESSED ..........................................

LAKES BY FISHERY BENEFICIAL USE ........................................................................................... 206

APPENDIX E – SURFACE WATER DISCHARGE PERMITS BY BASIN......................................... 212

APPENDIX F – PUBLIC COMMENTS ................................................................................................ 216

ii

Figure 1: Status of TMDLs from the 2006 Integrated Report ...................................................................... 20

Figure 2: Major River Basins in South Dakota............................................................................................. 44

Figure 3: 2008 South Dakota Waterbody Status .......................................................................................... 45

Figure 4: Bad River Basin ............................................................................................................................ 50

Figure 5: Belle Fourche River Basin ............................................................................................................ 62

Figure 6: Upper Big Sioux River Basin........................................................................................................ 81

Figure 7: Lower Big Sioux River Basin ....................................................................................................... 82

Figure 8: Upper Cheyenne River Basin........................................................................................................ 97

Figure 9: Lower Cheyenne River Basin ....................................................................................................... 98

Figure 10: Grand River Basin..................................................................................................................... 103

Figure 11: Upper James River Basin .......................................................................................................... 115

Figure 12: Lower James River Basin ......................................................................................................... 116

Figure 13: Little Missouri River Basin....................................................................................................... 119

Figure 14: Minnesota River Basin.............................................................................................................. 124

Figure 15: Upper Missouri River Basin...................................................................................................... 134

Figure 16: Lower Missouri River Basin ..................................................................................................... 135

Figure 17: Moreau River Basin .................................................................................................................. 139

Figure 18: Niobrara River Basin ................................................................................................................ 142

Figure 19: Red River Basin ........................................................................................................................ 145

Figure 20: Vermillion River Basin ............................................................................................................. 150

Figure 21: White River Basin..................................................................................................................... 156

Figure 22: Map Depicting Prairie Pothole Region ..................................................................................... 157

Figure 23: Status of TMDL Assessment and Implementation Projects...................................................... 177

Figure 24: South Dakota DENR Water Quality Monitoring Sites.............................................................. 201

Figure 25: Water Quality Monitoring Sites on Whitewood Creek and Tributaries

in Lead-Deadwood Area..................................................................................................................... 202

Figure 26: Water Quality Monitoring Sites Located on the Big Sioux River in the Sioux Falls Area ....... 203

Figure 27: Water Quality Monitoring Sites Located along the Cheyenne River and

White River that are Monitored for Uranium ..................................................................................... 204

Figure 28: Water Quality Monitoring Sites Located near the Grand River and Moreau River

that are Monitored for Uranium.......................................................................................................... 205

iii

Table 1. Atlas ................................................................................................................................................ 4

Table 2: Numeric Criteria Assigned to Beneficial Uses of Surface Waters of the State ARSD 74:51:01.... 10

Table 3: Surface Water Quality Standards for Toxic Pollutants and Total Ammonia ARSD 74:51:01 ....... 11

Table 4: Status of TMDLs from the 2006 Integrated Report........................................................................ 20

Table 5: 2008 Summary of TMDLs by Basin .............................................................................................. 22

Table 6: Sample Criteria for Determining Support Status............................................................................ 24

Table 7: South Dakota Fishery Beneficial Use Support Determination Range for Lakes............................ 28

Table 8: Designated Overall Use Support Status for Rivers and Streams in South Dakota ......................... 32

Table 9: Designated Overall Use Support Status for Lakes and Reservoirs in South Dakota ...................... 32

Table 10: Individual Use Support Summary for Rivers and Streams........................................................... 33

Table 11: Individual Use Support Summary for Lakes and Reservoirs ....................................................... 34

Table 12: Total Sizes of Water Impaired by Various Cause Categories in South Dakota............................ 35

Table 13: Total Sizes of Waters Impaired by Various Source Categories in South Dakota......................... 36

Table 14: Trophic Status of Significant Publicly Owned Lakes................................................................... 38

Table 15: Acid Effects on Lakes .................................................................................................................. 40

Table 16: Long Term Trends in Public Lakes (1989-2007) ......................................................................... 41

Table 17: Bad River Basin Information........................................................................................................ 48

Table 18: Belle Fourche River Basin Information........................................................................................ 52

Table 19: Big Sioux River Basin Information.............................................................................................. 64

Table 20: Cheyenne River Basin Information .............................................................................................. 85

Table 21: Grand River Basin Information .................................................................................................. 100

Table 22: James River Basin Information .................................................................................................. 105

Table 23: Little Missouri River Basin Information .................................................................................... 118

Table 24: Minnesota River Basin Information ........................................................................................... 121

Table 25: Missouri River Basin Information.............................................................................................. 126

Table 26: Moreau River Basin Information................................................................................................ 137

Table 27: Niobrara River Basin Information.............................................................................................. 141

Table 28: Red River Basin Information...................................................................................................... 144

Table 29: Vermillion River Basin Information........................................................................................... 147

Table 30: White River Basin Information .................................................................................................. 152

Table 31: Total Size Affected by Toxics.................................................................................................... 160

Table 32: Summary of Fish Kill Investigations (October 1, 2005 - September 30, 2007) ......................... 162

Table 33: Waterbodies Affected by Swimming Beach Closures................................................................ 164

Table 34: Waterbodies Affected by Fish and Shellfish Consumption Restrictions.................................... 166

Table 35: Waterbodies Affected by Domestic Water Supply Restrictions................................................. 167

Table 36: Summary of Waterbodies Not Fully Supporting Domestic Water Supply Use.......................... 167

Table 37: Summary of Domestic Water Supply Use Assessments for Streams ......................................... 168

Table 38: Summary of Domestic Water Supply Use Assessment for Lakes.............................................. 168

Table 39: South Dakota Categories and Subcategories of NPS Pollution Sources .................................... 176

1

This integrated 305(b) and 303(d) report (Integrated Report) was prepared by the South

Dakota Department of Environment and Natural Resources (DENR) pursuant to Sections

305(b), 303(d), and 314 of the Federal Water Pollution Control Act (P.L. 95-217).

The 305(b) report in previous years provided an assessment of the quality of South

Dakota’s water resources and summarized state programs established to prevent and

control water pollution. The 303(d) report identified impaired waterbodies within South

Dakota that require the development of Total Maximum Daily Loads (TMDLs). The

305(b) report was routinely used to create the 303(d) impaired waterbody list.

This document combines the 305(b) report and 303(d) list into one Integrated Report,

which provides an assessment of the quality of South Dakota's surface water resources

and identifies the impaired waterbodies that need TMDLs. It is the intent of this report to

inform the citizens of South Dakota and the US Environmental Protection Agency (EPA)

of the condition of state surface water resources and to serve as the basis for management

decisions by government and other entities for the protection of surface water quality.

EPA will use the information from the Integrated Report to document the state’s progress

in meeting and maintaining Clean Water Act goals for the ecological health of the

nation’s surface waters and their domestic, commercial, and recreational uses. DENR

will use the information in this report along with population data, economic analyses,

program capability assessments, and other appropriate information to plan and prioritize

water pollution control activities.

DENR will also use the Integrated Report as a tool to continue to stimulate development

of nonpoint source (NPS) projects and to produce a priority waterbody list for the

department. The Integrated Report will be available to all state conservation districts and

water development districts. Each district can review watershed information for its

geographical area of interest. This helps the districts focus on the location, nature, and

severity of surface water problems in their areas. This generally leads to public

discussions, which start the long process toward nonpoint source pollution control

implementation.

This report is shared with the Nonpoint Source Task Force to help focus its efforts and

provide information used in the priority waterbody ranking system. The Nonpoint

Source program also uses this document to supplement news articles released through the

DENR Information and Education (I&E) program.

The surface water quality assessments listed in this report rely primarily on the analyses

of data generated by DENR, the United States Geological Survey (USGS), water quality

data submitted by the cities of Watertown, Huron, and Sioux Falls, and best professional

judgment. While this assessment is as comprehensive as resources permit, some of the

state's surface water quality problems may not have been identified nor documented in

this report.

2

South Dakota Law (SDCL 34A-2-4 and 34A-2-6) authorizes the Department's Secretary

to provide this assessment of current state surface water quality to the people of the State

of South Dakota and the Environmental Protection Agency (EPA).

3

The purpose of this report is to assess the water quality of South Dakota's water resources

and to identify the impaired waterbodies that require TMDLs. This report meets the

requirements of Sections 305(b), 303(d), and 314 of the federal Clean Water Act which

mandates a biennial report on state water quality to Congress. This report is also intended

to inform the citizens of South Dakota on the status of the quality of their water

resources and to serve as the basis for management decisions by government staff and

local officials for the protection of water quality. DENR will use the information in this

report along with population data, economic analyses, program capability assessments,

and other appropriate sources to plan and prioritize water pollution control activities.

Surface Water Quality

South Dakota has about 9,289 miles of perennial rivers and streams (Table 1) and about

85,841 miles of intermittent streams. About 7,904 perennial stream miles have been

assessed in the past five years (October 2002 to September 2007). During this 5-year

interval, 49% of assessed stream miles were found to support all assigned beneficial uses

and 51% were nonsupporting of their designated uses. Seventy-seven percent of stream

miles designated for immersion recreation supported that beneficial use; 23% did not

meet the criteria. A total of 111 different streams or stream segments are listed as

impaired and require TMDL development.

Similar to previous reporting periods, nonsupport for fishery/aquatic life uses was caused

primarily by total suspended solids (TSS) from agricultural nonpoint sources (NPS) and

natural origin. Nonsupport for recreational uses was primarily caused by fecal coliform

contamination from livestock.

In addition to rivers and streams, South Dakota has 570 lakes and reservoirs with specific

aquatic life and recreational beneficial use classifications. The four Missouri River

mainstem reservoirs were not included in the total lake acres but were included in the

monitored river mileage.

An estimated 124 of the 570 classified lakes have been assessed. Eighteen lakes assessed

during the 2006 reporting cycle did not have sufficient data to determine support status

during this reporting cycle. The assessed lakes account for 65% of the total classified

lake acreage. An estimated 49% of the assessed lake acreage was considered to support

all assessed beneficial uses and 51% did not support assessed beneficial uses. A total of

57 lakes are listed as impaired and require TMDL development. Sediment and nutrients

conveyed in surface water runoff are the main nonpoint source pollutants impacting

South Dakota lakes and reservoirs.

DENR continues to conduct special chemical/physical/biological stream surveys and

ambient monitoring to assess the quality of receiving streams and to document water

quality problem sources and improvements.

4

State population (2000 census) 754,844

State surface area (sq. mi.) 77,047

Number of water basins (according to state subdivisions) 14

Total number of river/stream miles 95,130*

Number of perennial river miles (subset) 9,289*

Number of intermittent stream miles (subset) 85,841*

Number of border river miles of shared rivers/streams (subset) 360**

Miles of ditches and canals (man-made waterways) 424**

Number of classified lakes/reservoirs/ponds 570

Acres of lakes/reservoirs/ponds 204,987*

Square miles of estuaries/harbors/bays 0

Number of ocean coastal miles 0

Number of Great Lakes shore miles 0

Acres of freshwater wetlands 1,780,859***

Acres of tidal wetlands 0

Name of border rivers: Missouri River, Big Sioux River, Bois de Sioux River.

* Estimated from the National Hydrography Dataset (1:100,000 scale)

** (EPA, 1991)

*** National Wetlands Inventory

Wetlands

South Dakota has an estimated 1.78 million acres of small depressional wetlands with

shallow water habitat. South Dakota Surface Water Quality Standards contain provisions

to include wetlands as “waters of the state.” Wetlands are assigned the beneficial use of

fish and wildlife propagation, recreation, and stock watering, which provides protection

under existing narrative and numeric water quality standards.

The EPA is encouraging states to develop monitoring and assessment tools to determine

the ecological integrity of wetland environments. EPA currently promotes three

approaches to wetland assessment. South Dakota State University in cooperation with

South Dakota Game, Fish, and Parks (GF&P) is in the final stages of developing a Level-

1 and Level-2 wetland rapid assessment protocol for prairie pothole wetlands in eastern

South Dakota. The South Dakota wetland rapid assessment protocol will be used by the

State’s Natural Heritage and Wildlife Habitat Programs (GF&P) for identifying reference

wetlands, monitoring randomly selected sites and evaluating wetland restoration efforts.

A Level-3 wetland assessment was developed within the prairie pothole region of South

Dakota. An Index of Plant Community Integrity (IPCI) was used to evaluate the

5

vegetative composition of wetlands across classification (temporary and semipermanent)

and disturbance (native grass to cropland) gradients within the Northern Glaciated Plains

and Northwestern Glaciated Plains ecoregions. The IPCI method can be used in South

Dakota to allow the placement of wetlands into disturbance classes for ecological and

mitigation needs (Hargiss et al. 2007).

Water Pollution Control Programs

The water quality goals of the state are to: identify water quality problems, set forth

effective management programs for water pollution control, alleviate water quality

problems, and achieve and preserve water quality for all intended uses.

DENR continues to administer the National Pollutant Discharge Elimination System

(NPDES) program in South Dakota, referred to as the Surface Water Discharge

permitting program. The Surface Water Quality Program issues Surface Water Discharge

permits and develops water quality-based effluent limits to ensure water quality standards

are maintained.

Nonpoint Source (NPS) pollution originates from diverse and diffuse sources. Nonpoint

pollution controls must reflect this by wisely using resources available from various state,

federal, and local organizations plus have landowner support and participation. South

Dakota primarily uses voluntary measures for the implementation of Best Management

Practices (BMPs) to control NPS pollution. During the past 20 years, the program has

initiated many development and implementation projects throughout the state. The Clean

Water Act section 319 program is the focal point for a majority of the existing NPS

control programs.

Educating the public about NPS pollution issues has been effective in prompting many

landowners to voluntarily implement activities to control NPS pollution. However, the

technical and financial assistance currently available is not sufficient to solve all of the

NPS pollution problems in the state. Other solutions must be explored. Landowners

have the capability to accomplish much if they understand the problems and the methods

to solve them. Many of the solutions involve land management changes that benefit the

landowner by making their lands more productive and sustainable.

A total of 111 stream segments and 57 lakes require TMDLs to address impairments. Of

the total number of required TMDLs, 66% are for streams and 34% are for lakes.

6

General Discussion

South Dakota DENR monitors surface waters in the state through an established ambient

water quality sampling program, water quality surveys, fish surveys, TMDL assessments,

Surface Water Discharge permits, and state nonpoint source implementation projects.

The United States Geological Survey (USGS) also conducts routine monitoring

throughout the state. All data resulting from USGS monitoring efforts are available from

the USGS website. Most of the state’s data has been entered into the EPA data storage

and retrieval (STORET) system. DENR also maintains an internal database and will be

submitting data through EPA’s Water Quality Exchange (WQX) in the future. WQX will

be replacing STORET in 2009.

Water samples are analyzed for physical, chemical, biological, and bacteriological

parameters to provide baseline data for the determination of potential effects of point and

nonpoint sources of pollution. Baseline data are also used as a management tool to

determine the effectiveness of control programs on existing point and nonpoint sources

and for directing future activities. Water samples can show whether or not a waterbody is

meeting its assigned beneficial uses.

Water quality standards were first established for all surface waters by the state's

Committee on Water Pollution in 1967. The Water Management Board completed the

final steps of its most recent triennial review and revisions in July 2004, and EPA

formally approved South Dakota's water quality standard revisions on March 4, 2005.

The water quality standards consist of water quality criteria necessary to protect the

assigned beneficial uses of state surface waters.

All surface waters in the state are classified for one or more of the following beneficial

uses:

(1) Domestic water supply waters;

(2) Coldwater permanent fish life propagation waters;

(3) Coldwater marginal fish life propagation waters;

(4) Warmwater permanent fish life propagation waters;

(5) Warmwater semipermanent fish life propagation waters;

(6) Warmwater marginal fish life propagation waters;

(7) Immersion recreation waters;

(8) Limited contact recreation waters;

(9) Fish and wildlife propagation, recreation, and stock watering waters;

(10) Irrigation waters; and

(11) Commerce and industry waters.

7

All streams in South Dakota are assigned the beneficial uses (9) and (10) unless otherwise

stated in the Administrative Rules of South Dakota (ARSD) Chapter 74:51:03.

Lakes listed in ARSD Chapter 74:51:02 are assigned the beneficial uses of (7) and (8)

unless otherwise specified. All lakes in South Dakota are also assigned the beneficial use

of (9) unless otherwise stated in the same reference (74:51:02)

http://legis.state.sd.us/rules/rules/7451.htm. Table 2 contains a summary of the

established beneficial uses and a partial listing of assigned criteria to protect them.

Current state toxic pollutant standards for human health and aquatic life are presented in

Table 3.

Fixed Station Ambient Monitoring

The DENR water quality monitoring network is currently made up of 142 stations located

on various rivers and creeks within the state. Sampling stations are located within high

quality beneficial use classifications, above and below municipal/industrial discharges, or

within watersheds of concern. Currently, the department collects these samples on a

monthly, quarterly, or seasonal basis. This type of water sampling is invaluable for

monitoring historical information, natural background conditions, possible runoff events,

and acute or chronic water quality problems.

Typically, grab samples are collected mid-stream, either from a bridge or by wading into

the stream. Some stations may have to be sampled from the bank depending on

conditions. Every station is sampled in the same manner and location each time. When

the sample has been collected, the sampler immediately obtains water and air

temperatures, specific conductance, pH, and dissolved oxygen content. Time of sample,

water depth, channel width, and other visual observations are also recorded. The samples

are properly preserved and transported to the laboratory for analysis. Sample test results

are entered into DENR’s SQL NR92 database and EPA’s computer data storage and

retrieval system (STORET).

The most commonly sampled parameters include fecal coliform, hardness, alkalinity,

residue (total solids, total suspended solids, total dissolved solids), pH, ammonia, nitrates,

and phosphorous (total and dissolved). Several stations are sampled for sodium, calcium,

and magnesium during the irrigation season. Stations located along streams that receive

flows from historic Black Hills mining areas are also analyzed for cyanide, cadmium,

lead, copper, zinc, chromium, mercury, nickel, selenium, silver, and arsenic. Stations

along streams that receive flows from historic uranium mining or current exploration are

analyzed for arsenic, barium, molybdenum, uranium, radium 226, and radium 228.

Ambient station locations, descriptions, and schedules are included in Appendix C. More

detailed descriptions of individual stream sites are available from DENR on request.

Intensive Water Quality Monitoring (Point Sources)

Some of South Dakota’s wastewater treatment facilities are required to meet limits

beyond the federal technology-based effluent limits. For many of these permits, DENR

8

conducts an intensive water quality survey both above and below the wastewater

discharge. These surveys provide additional data to assist in the development of water

quality-based effluent limits for the Surface Water Discharge permits.

With increased emphasis on water quality improvements to justify federal expenditures,

the intensive monitoring program will also focus on showing water quality improvements

from the upgrading of wastewater treatment facilities. After wastewater treatment

facilities are upgraded, monitoring is used to verify that Surface Water Discharge permit

limits developed through computer modeling maintain or improve surface water quality.

Surveys provide an evaluation of whether or not the wastewater treatment is adequate to

protect the beneficial use(s) of receiving waters.

Intensive Water Quality Monitoring (Special Studies)

Intensive water quality monitoring is sometimes initiated to assess special problem areas,

to obtain data for use in site-specific criteria modification studies, or to provide an

updated database for a waterbody. In 2004 and 2005, DENR developed a special water

quality monitoring plan for the Missouri River reservoirs. The focus of the plan was to

develop a long term monitoring strategy to determine beneficial use support. Intensive

sampling of the reservoirs was performed in 2005 and 2006. Data analyses are currently

underway and the preliminary results will be included in the 2010 Integrated Report.

Intensive Fish Survey Monitoring

Fish surveys are occasionally conducted by DENR Surface Water Quality Program and

GF&P to evaluate the impact of wastewater dischargers on the receiving stream and to

evaluate the fishery classification. The fish survey results, although they are qualitative in

nature, are used in conjunction with water quality surveys to evaluate the impact of

pollutants on stream water quality.

Biological Sampling Program

Biological samples are often included as part of a watershed assessment study or a special

study. DENR Water Resource Assistance Program incorporates aquatic plant/algae

incorporate bioassessment surveys using fish and aquatic invertebrates as primary water

quality indicators.

9

Toxicity Testing Program

Priority toxic pollutants are relatively expensive to analyze and are not routinely

monitored except for special situations. Whole effluent toxicity tests have been included

as permit limits in many municipal and industrial Surface Water Discharge permits.

10

1 30-day average 2 daily maximum

Parameters

(mg/L) except

where noted

(1)

Domestic

water supply

(2)

Coldwater

permanent

fish life

propagation

(3)

Coldwater

marginal fish

life

propagation

(4)

Warmwater

permanent fish

life propagation

(5)

Warmwater

semipermanent

fish life

propagation

(6)

Warmwater

marginal fish

life

propagation

(7)

Immersion

recreation

(8)

Limitedcontact

recreation

(9)

Fish, wildlife

propagation,

recreation &

stock watering

(10)

Irrigation

(11)

Commerce

and Industry

Alkalinity

(CaCO3)

7501/1,3132

Barium 1.0

Chloride 2501/4382 1001/1752

Chlorine, total

residual

0.019 acute

0.011chronic

0.019 acute

0.011chronic

0.019 acute

0.011chronic

0.019 acute

0.011chronic

0.019 acute

0.011chronic

Coliform, total

(per 100 mL)

5,000 (mean);

20,000 (single

sample)

Coliform, fecal

(per 100 mL)

200 (mean);

400 (single

sample)

1,000 (mean);

2,000 (single

sample)

Conductivity

(umhos/cm @

25°C)

4,0001/7,0002 2,5001/

4,3752

Fluoride 4.0

Hydrogen

sulfide,

undisassociated

0.002 0.002 0.002 0.002 0.002

Nitrogen, total

ammonia as N

Equationbased

limit 1, 2

Equationbased

limit1, 2

Equation-based

limit 1, 2

Equation-based

limit1, 2

Equationbased

limit1, 2

Nitrogen,

nitrates as N

10.0 501/882

Oxygen,

dissolved

> 6.0;

> 7.0 (during

spawning

season)

> 5.0 > 5.0;

> 6.0 (in Big

Stone Lk & Lk

Traverse during

Apr & May)

> 5.0 > 4.0 > 5.0 > 5.0

pH ( standard

units)

6.5 – 9.0 6.6 – 8.6 6.5 – 8.8 6.5 – 9.0 6.5 – 9.0 6.0 – 9.0 6.0 – 9.5 6.0 – 9.5

Sodium

Adsorption

Ratio

10

Solids, total

suspended

301/532 901/1582 901/1582 901/1582 1501/2632

Solids, total

dissolved

1,0001/1,7502 2,5001/4,3752 2,0001/3,500

2

Sulfate 5001/8752

Temperature

(°F)

65 75 80 90 90

Total Petroleum

Hydrocarbons

< 1.0 < 10

Oil and Grease < 10

11

Pollutant

Human Health Value

Concentrations in ug/L

Freshwater Aquatic

Life Value

Concentrations in

ug/L

Uses 2-3-4-5-6-9

Pollutant

Human Health Value

Concentrations in ug/L

Freshwater Aquatic

Life Value

Concentrations in

ug/L

Uses 2-3-4-5-6-9

Use

1(3)

Uses

2-3-4-5-

6-9(4)

Acute

(CMC)

Chronic

(CCC) Use

1(3)

Uses

2-3-4-5-

6-9(4)

Acute

(CMC)

Chronic

(CCC)

Acenaphthene 670 990 2,4-Dimethylphenol 380 850

Acenaphthylene (PAH)(6) Dimethyl Phthalate 270,000 1,100,000

Acrolein 190 290 Di-n-Butyl-Phthalate 2,000 4,500

Acrylonitrile(5) 0.051 0.25 2-Methyl-4,6-

Dinitrophenol

13 280

Aldrin(5) 0.000049 0.000050 1.5 2,4-Dinitrophenol 69 5,300

Anthracene (PAH)(6) 8,300 40,000 Dioxin (2,3,7,8-

TCDD(5)

5.0E-9 5.1E-9

Antimony 5.6 640 2,4-Dinitrotoluene(5) 0.11 3.4

Arsenic(5) 0.018(5)(13) 0.14(5)(13) 340 150 1,2-

Diphenylhydrazine(5)

0.036 0.20

Asbestos(5) 7,000,000

fibers/L

alpha-Endosulfan 62 89 0.11 0.056

alpha-BHC(5) 0.0026 0.0049 beta-Endosulfan 62 89 0.11 0.056

beta-BHC(5) 0.0091 0.017 Endosulfan Sulfate 62 89

gamma-BHC (Lindane)(5) 0.98 1.8 0.95 Endrin 0.059 0.060 0.086 0.036

Benzene(5) 2.2 51 Endrin Aldehyde 0.29 0.30

Benzidine(5) 0.000086 0.00020 Ethylbenzene 530 2,100

Benzo(a)Anthracene(5) 0.0038 0.018 Flouranthene 130 140

Benzo(a)Pyrene(5) 0.0038 0.018 Fluorene(6) 1,100 5,300

Benzo(b)Fluoroanthene(5) 0.0038 0.018 Heptachlor(5) 0.000079 0.000079 0.26 0.0038

Benzo(k)Flouroanthene(5) 0.0038 0.018 Heptachlor epoxide(5) 0.000039 0.000039 0.26 0.0038

Beryllium(5) 4(14) Hexachlorobenzene(5) 0.00028 0.00029

Bis(2-Chloroethyl)Ether(5) 0.030 0.53 Hexachlorobutadiene(5) 0.44 18

Bis(2-

Chloroisopropyl)Ether

1,400 65,000 Hexachlorocyclopentadi

ene

40 1,100

Bis(2-

Ethylhexyl)Phthalate(5)

1.2 2.2 Hexachloroethane(5) 1.4 3.3

Bromoform(6) 4.3 140 Ideno(1,2,3-cd)Pyrene 0.0038 0.018

Butylbenzyl Phthalate 1,500 1,900 Isophorone(5) 35 960

Cadmium 2.0(9) 0.25(9) Lead 65(9) 2.5(9)

Carbon Tetrachloride(5) 0.23 1.6 Mercury 0.050 0.051 1.4 0.012(10)

Chlordane(5) 0.00080 0.00081 1.2 0.0043 Methyl Bromide 47 1,500

Chlorine 19 11 Methyl Chloride(6)

Chlorobenzene 130 1,600 Methylene Chloride(5) 4.6 590

Chlorodibromomethane(5) 0.40 13 NNitrosodimethylamine(

5)

0.00069 3.0

Chloroform(5) 5.7 470 N-Nitrosodi-n-

Propylamine(5)

0.0050 0.51

2-Chloronaphthalene 1,000 1,600 NNitrosodiphenylamine(

5)

3.3 6.0

2-Chlorophenol 81 150 Nickel 610 4,600 470(9) 52(9)

Chromium(III) 570(9) 74(9) Nitrobenzene 17 690

Chromium(VI) 16 11 Polychlorinated

Biphenyls,

PCBs(2)(5)(7)(11)

0.00006

4

0.000064

0.014

Chrysene(5) 0.0038 0.018 Pentachlorophenol 0.27 3.0 19(8) 15(8)

Copper 1,300 13(9) 9.0(9) Phenanthrene(6)

Cyanide (week acid

dissociable)

140 140 22 5.2 Phenol 21,000 1,700,00

0

4,4'-DDD(5) 0.00031 0.00031 Pyrene(6) 830 4,000

4,4'-DDE(5) 0.00022 0.00022 Selenium(7) 170 4,200 (12) 4.6

4,4'-DDT(5)(7) 0.00022 0.00022 0.55 0.001 Silver 3.2(9)

Dibenzo(a,h)Anthracene(5) 0.0038 0.018 1,2,4-Trichlorobenzene 35 70

1,2-Dichlorobenzene 420 1,300 1,1,2,2-

Tetrachloroethane(5)

0.17 4.0

12

Pollutant

Human Health Value

Concentrations in ug/L

Freshwater Aquatic

Life Value

Concentrations in

ug/L

Uses 2-3-4-5-6-9

Pollutant

Human Health Value

Concentrations in ug/L

Freshwater Aquatic

Life Value

Concentrations in

ug/L

Uses 2-3-4-5-6-9

Use

1(3)

Uses

2-3-4-5-

6-9(4)

Acute

(CMC)

Chronic

(CCC) Use

1(3)

Uses

2-3-4-5-

6-9(4)

Acute

(CMC)

Chronic

(CCC)

1,3-Dichlorobenzene 320 960 Tetrachloroethylene(6) 0.69 3.3

1,4-Dichlorobenzene 63 190 Thallium 0.24 0.47

3,3'-Dichlorobenzidine(5) 0.021 0.028 Toluene 1,300 15,000

Dichlorobromomethane(6) 0.55 17 Toxaphene(5) 0.00028 0.00028 0.73 0.0002

1,2-Dichloroethane(5) 0.38 37 1,2-Trans-

Dichloroethylene

140 10,000

1,1-Dichloroethylene(5) 330 7,100 1,1,1-Trichloroethane

2,4-Dichlorophenol 77 290 1,1,2-Trichloroethane(5) 0.59 16

1,2-Dichloropropane(5) 0.50 15 Trichloroethylene(5) 2.5 30

1,3-Dichloropropene 0.34 21 2,4,6-Trichlorophenol(5) 1.4 2.4

Dieldrin(5) 0.000052 0.000054 0.24 0.056 Vinyl Chloride(5) 0.025 2.4

Diethyl Phthalate 17,000 44,000 Zinc 7,400 26,000 120(9) 120(9)

mercury (acute), nickel, selenium, silver and zinc given in this document refer to the dissolved

amount of each substance unless otherwise noted. All Surface Water Discharge permit effluent

limits for metals shall be expressed and measured in accordance with § 74:52:03:16.

pollutants as previously established in §§ 74:51:01:31, 74:51:01:32, 74:51:01:44 to 74:51:01:54,

inclusive, and § 74:51:01:56.

water.

class of chemicals with carcinogenicity as the basis for the criteria derivation for that class of

chemicals; an individual carcinogenicity assessment for these chemicals is pending.

13

each case must be calculated using the following equation taken from National Recommended

Water Quality Criteria: 2002 (EPA-822-R-02-047, November 2002):

hardness of 100 mg/L. Criteria for each case must be calculated using the following equations

taken from National Recommended Water Quality Criteria: 2002 (EPA-822-R-02-047, November

2002):

*Conversion factors are hardness-dependent. The values shown are with a hardness of 100 mg/L

the following equations:

Chronic: CF = 1.101672 - [(ln hardness)(0.041838)]

Acute: CF = 1.136672 - [(ln hardness)(0.041838)]

*Conversion factors are hardness-dependent. The values shown are with a hardness of 100 mg/L

the following equations:

Acute and Chronic: CF = 1.46203 - [(ln hardness)(0.145712)]

14

analyses).

15

Equation 1: For waters where salmonid fish are present.

pH = the pH of the water quality sample in standard units.

Equation 2: For waters where salmonid fish are not present.

pH - the pH of the water quality sample in standard units.

Equation 3: For waters where early life stages are present.

T = the water temperature of the sample in degrees Centigrade.

pH - the pH of the water quality sample in standard units.

Equation 4: For waters where early life stages are absent.

T = the water temperature of the sample in degrees Centigrade.

pH = the pH of the water quality sample in standards units.

MAX = use either the water temperature (T) for the sample, or 7, whichever is the greater

value.

16

Total Maximum Daily Loads (TMDLs) and Section 303(d)

TMDLs are an important tool for the management and protection of South Dakota’s

surface water quality. The goal of TMDLs is to ensure that waters of the state attain and

maintain water quality standards, and support their beneficial uses. EPA defines a

TMDL as “the sum of the individual waste load allocations for point sources and load

allocations for both nonpoint sources and natural background sources established at a

level necessary to achieve compliance with applicable surface water quality standards.”

In simple terms, a TMDL is the amount of pollution a waterbody can receive and still

support its assigned beneficial uses.

TMDLs must be developed for impaired waters, should address a specific waterbody or

watershed, and should specify quantifiable targets and associated actions that will enable

a given waterbody to support its assigned beneficial uses.

Section 303(d) of the federal Clean Water Act (CWA) requires states to develop and

submit for approval a list of waters targeted for TMDL development every two years.

This is referred to as the 303(d) list. Items that must accompany this list include targeted

pollutants and timeframes for TMDL development.

Once identification of TMDL waters are completed, states are to develop TMDLs at a

pace necessary to complete all the TMDLs during a 13 year period. TMDLs must allow

for seasonal variations and a margin of safety that accounts for any lack of knowledge

concerning the relationship between pollutant loadings and water quality.

The following information and data sources were used to determine which waterbodies

require TMDLs based on the requirements of section 303(d) of the federal Clean Water

Act:

also known as “impaired” waters;

and

local, state, or federal agencies; the general public; or academic institutions.

Waters that are considered impaired for the assigned beneficial uses require a TMDL.

This includes waters that are identified under the “not supporting” beneficial use

categories in this report unless the waterbody has a recent TMDL approved by EPA that

addresses the impairments.

17

In 1993, DENR was delegated the authority to administer the National Pollutant

Discharge Elimination System (NPDES) permitting program. As stated earlier, South

Dakota’s NPDES permitting program is referred to as the Surface Water Discharge

(SWD) permitting program. SWD permits are used to control the discharge of pollutants

from point sources. At a minimum, most SWD permits contain technology-based effluent

limits, which are attained using the best available technology that is economically

achievable. However, in some cases, the application of technology-based effluent limits

is not sufficient to ensure the surface water quality standards are maintained. For these

permits, DENR develops water quality-based effluent limits for the permit.

If a SWD permittee discharges a pollutant to an impaired waterbody, the TMDL for that

pollutant will include a “wasteload allocation” for the permittee. The wasteload allocation

is implemented through the SWD permit.

SWD permits are issued for a maximum of five years, after which time the effluent limits

and existing in-stream water quality are reevaluated. Ammonia, biochemical oxygen

demand (BOD), and dissolved oxygen are the primary parameters targeted for modeling

to develop water quality-based effluent limit. As can be seen from this report, very few

streams have impairments for ammonia or dissolved oxygen. Therefore, South Dakota’s

point source control program has been effective at maintaining and improving the quality

of surface waters in the state.

SDDENR received a letter from the South Dakota Resources Coalition requesting that

Lake Cochrane be placed on the impaired waterbodies list due to nutrient concerns. A

description of the request and DENR’s response is included in Appendix F.

Prioritization of TMDL Waters

prioritization process.

A system of prioritization has been developed by DENR based on several factors.

meeting the following criteria (Priority 1):

18

improvement.

Priority 2 waters meet the following criteria:

consideration given to the rapidity of the declining water quality;

documented;

These criteria are a guide. If a waterbody met any one criteria in a category that did not

necessarily mean the waterbody was prioritized as such, since many waterbodies fit one

or more criteria from the lists above.

Section 319 TMDL assessments are developed based upon the prioritization criteria listed

above. Section 319 TMDLs are developed as part of an assessment project. DENR

prefers to develop TMDLs in 12 digit hydrologic units or larger “clusters” that include all

nonpoint source TMDLs required for a river basin. For larger basins, such as the Big

Sioux, studies are completed by dividing the basin into sub-basins. Watershed

implementation projects for completed nonpoint source TMDL assessments also follow

the “clustering” format within associated river basins or sub-basins. Implementation

projects for completed TMDL assessments hinge upon whether adequate local support

exists. For more information on nonpoint source TMDL development and

implementation refer to the “South Dakota Nonpoint Source Program Management

Plan”. This document is located at the following web link:

http://www.state.sd.us/denr/DFTA/WatershedProtection/NPSMgmtPlan07.pdf

The priorities for developing water quality-based effluent limits are not based upon the

severity of waterbody impairment but upon the importance of maintaining water quality

improvements made through the permits.

Summary of the State TMDL Waterbodies

Using the methodologies, data, information, and public input described for the surface

water quality assessments, DENR included the waterbodies that require TMDLs

(previously known as the 303(d) list) in Tables 17 - 30. The tables include waterbody

names, pollutants of concern, basis for listing, and other information. A total of 168

different waterbodies require TMDLs (Table 5). Each waterbody may contain several

19

different pollutants and thereby may constitute several TMDLs. In addition, some

streams are listed more than once due to TMDLs identified for different segments of the

same stream (even for the same pollutant).

If a specific waterbody required a TMDL for several different pollutants, all pollutants

were grouped into one TMDL for that waterbody. In reality, it may not be possible to

incorporate each pollutant into a single TMDL for each waterbody segment, but this

assumption was made for planning purposes. There may be other cases where widespread

support for water quality improvement, large single entity landholders (federal lands,

state lands, etc.), or other factors allow several waterbodies to be targeted for

improvement under a single TMDL. Possible scenarios such as these make TMDL

numbers difficult to project. Notwithstanding this fact, the implications of the list are that

a monumental work effort will be required to complete the number of TMDLs in the time

frame suggested by the list.

TMDL issues span a wide range of activities within DENR. Nonpoint source

assessments, clean lakes assessments, discharge permitting, water quality monitoring,

water quality standards, water rights, feedlot regulations, and other areas are involved in

or affect TMDL development and implementation. Because of this, the development and

implementation of TMDLs will rely on existing programs, resources, and activities.

Effective TMDL development requires good coordination within all DENR water

programs. In addition, the development and implementation of effective TMDLs that will

result in improving the quality of South Dakota’s waters must have the support, input,

and coordination of affected government agencies, local groups, and citizens. As such,

the TMDL effort will involve the coordination of many diverse groups and the public,

with the common goal of improving water quality.

It is not possible to develop TMDLs for every waterbody within two years. The time

frame to develop TMDLs on each biennial list is 13 years in accordance with EPA

guidelines.

20

South Dakota’s 2006 list contained 147 different waterbodies or waterbody segments for

TMDL development. A total of 30 TMDLs have been completed or determined to be

unnecessary by DENR since April 1, 2006. Table 4 and Figure 1 below show the status

of waters that required TMDLs in the 2006 Integrated Report.

TMDLs in Progress

53%

TMDLs Planned

27%

Delisted Based on

New Information

9%

TMDL Approved

11%

21

Delisting of Certain 2006 TMDL Waters and Other Exclusions

Waters were delisted using the following criteria:

- New monitoring data show attainment; or

- New modeling results show no potential for exceedance of standards.

22

Table 5 is a list of the projected number of TMDLs required in each basin and the

associated pollutants of concern. Watershed assessments are currently underway in

several basins. Several of these assessment efforts have identified additional impaired

reaches that were not previously recognized in the 2006 Integrated Report. Although

there is an increase in TMDLs from 2006 to 2008, many of these reaches have current

TMDL development in progress.

Bad River

Basin 4 Nutrients, bacteria, total dissolved solids, specific conductance

Belle Fourche

River Basin 16 Bacteria, metals, pH, temperature, specific conductance

Big Sioux

River Basin 44 Bacteria, mercury in fish tissue, dissolved oxygen, nutrients, total

suspended solids, pH

Cheyenne

River Basin 35

Bacteria, nutrients, pH, temperature, sodium adsorption ratio, total

suspended solids, total dissolved solids, sulfates, dissolved oxygen,

specific conductance

Grand River

Basin 9

Bacteria, mercury in fish tissue, nutrients, sodium adsorption ratio,

temperature, total suspended solids, total dissolved solids, specific

conductance, pH

James River

Basin 23 Ammonia, bacteria, dissolved oxygen, nutrients, pH, total suspended

solids, total dissolved solids, temperature

Little Missouri

River Basin 0

Minnesota

River Basin 1 Dissolved oxygen

Missouri River

Basin 16 Bacteria, mercury in fish tissue, dissolved oxygen, nutrients, total

suspended solids, total dissolved solids, specific conductance, pH

Moreau River

Basin 5 Bacteria, dissolved oxygen, total suspended solids, sodium adsorption

ratio, total dissolved solids, specific conductance

Niobrara River

Basin 2 Nutrients, total suspended solids, bacteria

Red River

Basin 1 Nutrients

Vermillion

River Basin 6 Bacteria, nutrients, total suspended solids, pH, mercury in fish tissue

White River

Basin 6 Bacteria, total suspended solids, temperature

23

Two major types of assessments were used to determine use support status of

waterbodies; one based on monitoring and the other based on qualitative evaluations.

Monitoring data were primarily obtained from DENR, USGS, the city of Huron, the city

of Watertown, and the city of Sioux Falls. Sources of quantitative and qualitative lake

assessment data were acquired from the Statewide Lakes Assessment project and

individual assessment studies.

DENR maintains a Quality Assurance/Quality Control (QA/QC) Program to ensure that

all environmental water quality data generated or processed meet standard accepted

requirements for precision, accuracy, completeness, representativeness, and comparability.

This entails the preparation and periodic review and revision of the DENR

Quality Assurance Program and individual project plans. It also includes the preparation

of periodic reports to DENR management and EPA; the review of contracts, grants,

agreements, etc., for consistency with QA/QC requirements; and the administration of

QA/QC systems and performance audits. The latter activity requires the establishment of

schedules for the collection of the duplicate and blank samples, periodic testing of field

sampling techniques and liaison with contracted labs to ensure compliance with QA/QC

objectives. In 1998, the Water Resources Assistance Program created a QA/QC document

and protocol for its Clean Lakes and NPS programs. An updated Standard

Operating Procedure manual was completed and published in February 2005.

The ambient monitoring station assessment network provides useful information on

overall stream water quality. Only a brief summary of water quality is included because

of the large volume of data and reports. A more detailed description of the stream

ambient monitoring program is found in the preceding Surface Water Quality Monitoring

Program chapter of this document.

Fixed station monitoring data were assessed by dividing major streams into segments that

contain the same or similar designated beneficial uses, water quality standards criteria,

and environmental and physical influences. Data obtained during the current reporting

period were analyzed by utilizing DENR’s NR92 Database system. The data for each

monitored segment were compared to state water quality standards applicable to the

beneficial uses assigned to the segment in question (Tables 2 and 3). Monitored stream

course mileages and lake acreages were measured using EPA Reach Indexing Tool

software.

Specific criteria were developed to define how data for streams would be evaluated to

determine the status of each stream segment (waterbody). The following criteria were

used:

24

FOR CONVENTIONAL PARAMETERS

(such as dissolved oxygen, total suspended

solids, pH, water temperature, etc.)

Number of observations (samples) required

to consider data representative of actual

conditions

STREAMS: at least 20 samples for any one parameter

are usually required at any site. The sample threshold

was reduced to 10 samples if greater than 25% of

samples exceed water quality standards since

impairment is more likely. In addition, the sample

threshold was reduced to five samples if 100% of the

samples indicated full or nonsupport for that parameter.

LAKES: 2 separate years of samples for conventional

and Trophic State Index (TSI) parameters. Must include

Sample dates must be between May 15 and September

15.

FOR CONVENTIONAL PARAMETERS

Required percentage of samples exceeding

water quality standards in order to consider

segment water quality-limited

STREAMS: >10% (>25% if less than 20 samples

available).

LAKES: >10% of surface samples (>25% if less than 20

samples available).

If one surface exceedance was observed for water

temperature, dissolved oxygen, or pH; lake profile data

was used to make listing determinations. Lakes were

considered fully supporting the aquatic life beneficial

use if profile data indicate a region within the water

column where temperature, pH, and dissolved oxygen

were meeting numeric water quality standards. If a

region did not exist the lake was listed for the parameter

in exceedance.

FOR TOXIC PARAMETERS (such as

metals, mercury, total ammonia, etc.)

Number of observations (samples) required

STREAMS: At least one water quality sampling event.

LAKES: At least one fish flesh sampling event.

FOR TOXIC PARAMETERS

Required percentage of samples exceeding

water quality standards in order to consider

segment water quality-limited

STREAMS: More than one exceedance of toxic criteria

within the past 3 years.

LAKES: If fish flesh samples are above the Federal

Drug Administration’s recommended action levels (such

as 1 part per million for mercury).

Data age (for both conventional and toxic

parameters)

STREAMS: Data must be less than five years old.

LAKES: Data collected from 2000-2007

Unless there is justification that data is (or is not)

representative of current conditions. While a data age of

two years matches the report cycle, it does not allow for

enough samples to accurately portray variability.

Quality Assurance/Quality Control (for

both conventional and toxic parameters)

STREAMS and LAKES: There must be a consensus that

the data meets QA/QC requirements similar to those

outlined in DENR protocols. QA/QC data was

encouraged to be submitted.

25

Waterbodies were also considered nonsupporting if beach closures were attributable to

pollution related causes. Waterbodies were listed as nonsupporting through beach

closures where there were more than three beach closures per season in a consecutive

three week sampling period based on fecal coliform concentrations.

Deviations from the above criteria were allowed in specific cases, and are generally

discussed in the proceeding tables listing the surface water quality summaries. Use

support assessment for all assigned uses was based on the number of exceedances of

water quality standards for the following parameters: total suspended solids, total

dissolved solids, pH, water temperature, dissolved oxygen, fecal coliform, and others.

Exceedances of more than one parameter were not considered additive in determining

overall support status for any given waterbody. A stream segment with less than 10%

exceedances with respect to the total number of samples for one or more parameters is

considered fully supporting. Complete listings of relevant parameters appear in Tables 2

and 3. South Dakota has established the following general criteria for determining use

support of monitored streams:

In order to ensure a sufficient number of samples was available for each stream segment

(usually a minimum of 20) to arrive at an assessment that would be statistically

acceptable, the period of record considered for this report was from October 1, 2002, to

September 30, 2007, (5 years) for streams and May 15, 2000, to September 15, 2007, (8

years) for lakes. The lake’s date range was changed from that of past reporting cycles.

The eight year timeframe covers data from at least two sampling rotations to provide a

more recent description of a lake’s support status between reporting cycles.

Much of the waterbody impairment information is summarized in Tables 7 through 16.

More detailed information on the lakes and streams in each river basin is presented in

Tables 17 through 30.

In addition to the use support assessment above, South Dakota has chosen to use the

assessment categories that EPA recommends in its guidance that was issued on July 21,

2003. South Dakota’s assessment categories are as follows:

26

Category 1: All designated uses are met;

Category 2: Some of the designated uses are met but there is insufficient data to

determine if remaining designated uses are met;

Category 3: Insufficient data to determine whether any designated uses are met;

Category 4A: Water is impaired but has an EPA approved TMDL;

Category 4B: Water is impaired but implementation project (best management

practices) is in place;

Category 4C: Water is impaired by a parameter that is not considered a

“pollutant;”

Category 5: Water is impaired or threatened and a TMDL is needed.

Support assessment for fish and aquatic life propagation use primarily involves

monitoring the following major parameters: dissolved oxygen, total ammonia, water

temperature, pH, and total suspended solids.

Support assessment for immersion recreation and limited contact recreation involves

monitoring dissolved oxygen and fecal coliform. Fecal coliform is monitored from May

1 through September 30 of each year (Table 2).

South Dakota adopted numeric surface water quality criteria with the 1967 “Water

Quality Standards for the Surface Waters for the State of South Dakota.” The main intent

of numeric water quality criteria is to regulate discharges of wastewater from industries

and municipal wastewater treatment facilities. Numeric criteria are needed to develop

numeric effluent limits for facilities that discharge wastes to surface water. However,

since South Dakota has numeric water quality criteria, a strict interpretation of the water

quality standards could imply that a waterbody could potentially be listed as “impaired”

or “nonsupporting” even if only one exceedance occurred within a five year period.

South Dakota and even EPA have traditionally viewed the 10% approach (as stated in the

criteria for determining support status in Table 6) as an appropriate measuring tool to

determine waters that require further in-depth study and TMDL development. Factors

such as drought, high precipitation events, and other environmental factors can cause

significant variation in water quality. One exceedance of a conventional parameter, such

as pH or water temperature, does not indicate a waterbody is not supporting its beneficial

use. The methodology employed by the department in the interpretation of the data for

the 2008 Integrated Report is consistent with DENR’s interpretation of the South Dakota

Surface Water Quality Standards. Therefore, for the Integrated Report purposes, DENR

defines “impairment” or “nonsupport” of a beneficial use of a waterbody by the criteria

found in Table 6.

Lake water quality data is acquired from the DENR’s Statewide Lakes Assessment

(SWLA) project. Lakes are sampled on a four year rotation (i.e. about 31 lakes annually)

twice during the growing season, at one to three predetermined site locations. The

number of site locations assigned to each lake is dependent on basin size. Field

measurements are collected and water samples are composited from each site. Lake data

27

available from 2000 through the 2007 sampling season were used to make support

determinations for this report.

Data collected during the growing season (May 15 - September 15) from individual lake

assessment projects is also used to supplement the SWLA data. Project specific data is

usually collected monthly throughout the growing season from site locations consistent

with those established during the SWLA project. Field measurements and water samples

citizens’ monitoring efforts.

A group of 17 standard water quality parameters are measured or analyzed. Water

temperature, dissolved oxygen, conductivity, specific conductance, pH and Secchi disk

sample and analyzed by spectrophotometer as described by APHA (1995). The

remaining samples are preserved, iced and shipped to the State Health Laboratory in

Pierre, South Dakota, for individual parameter analysis.

For the 2008 reporting cycle, support status of lakes and reservoirs was evaluated based

on trophic state indicators and water quality standard limits. The Trophic State Index

(TSI) approach (Carlson 1977), represents an impairment targeting criteria, designed to

augment narrative criteria for making lake support determinations. All available Secchi

TSI value for each lake based on a minimum of two years data.

The fishery beneficial use designation was used as a classification tool to define the

support status of lakes. A document explaining the rationale and methodology of the

current TSI approach for Targeting Impaired Lakes in South Dakota is located on the

DENR website at:

http://www.state.sd.us/denr/Documents/ImpairedLakes.pdf

were derived from statistical analysis and Best Professional Judgment (BPJ). TSI values

are based on the median of all available data and not individual data values. If the

median TSI value exceeded the support criteria in Table 7, the waterbody was listed as

nonsupporting the fishery beneficial use. Appendix D depicts the calculated median TSI

beneficial use.

28

Beneficial Use Fully Supporting Not Supporting

Coldwater Permanent Fish Life

Propagation

Coldwater Marginal Fish Life

Propagation

Warmwater Permanent Fish Life

Propagation

Warmwater Semipermanent Fish Life

Propagation

Warmwater Marginal Fish Life

Propagation

In addition to the TSI values, lake support status was evaluated using state water quality

standards. State water quality standard numeric criteria provide a benchmark for making

listing decisions. However, water quality is variable and dependent on the environmental

conditions present during sample collection. To account for variability, all available

surface data collected during the growing season from 2000-2007 was used to identify

parameter specific impairments for individual assessed lakes.

Fish and other aquatic life are relatively mobile and can move vertically within the water

column to escape adverse conditions. If one surface exceedance was observed for water

temperature, dissolved oxygen, or pH, lake profile data was used to make listing

determinations. Lakes were considered fully supporting the aquatic life beneficial use if

profile data indicate a region within the water column where temperature, pH, and

dissolved oxygen were meeting numeric water quality standards. If a region did not exist

the lake was listed for the parameter in exceedance.

Parameters such as nitrate, ammonia-nitrogen, specific conductance, total dissolved

solids, total suspended solids and alkalinity not collected in the profile were listed based

on the criteria found in Table 6 depending on the number of data available for a given

lake.

29

Waterbodies were also evaluated based on beach closures, fish kills, and fish

consumption advisories. Beach closure information collected during this reporting period

(2006-2007) was used to make impairment decisions (Table 32). Lakes were listed if

three beach closures per season occurred in a consecutive three week sampling period. A

public beach is recommended for closure if the following fecal coliform levels are met.

(1) Any three consecutive samples exceed 200 fecal coliform per 100

milliliters;

(2) Any two consecutive samples exceed 300 fecal coliform per 100

milliliters; or

(3) Any single sample exceeds 1,000 fecal coliform per 100 milliliters.

Long term trends in TSI were estimated from data collected during the 1989 through

2007 statewide lake assessments and from individual assessment projects. A slope of +

five units between respective TSI values was selected as signifying a legitimate change in

lake water quality over the course of data availability. Long term trends covering the

period from 1989 through 2007 are summarized in the Lake Water Quality Assessment

chapter of this section (Table 16).

30

South Dakota has a total of about 9,289 miles of perennial rivers and streams (Table 1).

Major or significant streams in this context are waters that have been assigned aquatic life

use support in addition to the beneficial uses of fish and wildlife propagation, recreation,

stock watering (9), and irrigation (10). This definition includes primary tributaries and,

less frequently, subtributaries of most state rivers and larger perennial streams. In a few

cases, lower order tributaries may be included, for example in the Black Hills area, which

has a relatively large number of permanent streams.

Approximately 7,904 miles of perennial streams have been assessed to determine water

quality status for a period covering the last five years (October 2002 through September

2007). Data needed to be evaluated over this longer time span to ensure enough data

points were available for each stream segment (usually 20) to properly characterize

existing stream conditions. Since some stream segments had only four (or fewer)

samples available per year, evaluation of a data set covering at least five years of

sampling was required to adequately portray the natural variability in water quality that is

typical of stream environments.

Currently, 49% of the assessed stream miles fully support all assigned beneficial uses and

51% do not presently support one or more uses. The high percentage of impairment can

be attributed largely to high levels of total suspended solids (TSS) and fecal coliform.

During this reporting cycle, 6,700 designated miles were assessed for fishery/aquatic life

beneficial use attainment; 56% of assessed stream miles fully met fishery/aquatic life

criteria, while 44% did not. 2,295 miles were also assessed for immersion recreation

attainment. Seventy-seven percent fully supported immersion recreation criteria, while

23% did not.

Nonsupport in assessed streams was caused primarily by total suspended solids from

agricultural nonpoint sources and natural origin. In approximate order of stream miles

affected, additional causes of impairment this reporting cycle include: fecal coliform,

water temperature, sodium adsorption ratio, specific conductance, total dissolved solids,

and low concentrations of dissolved oxygen. Natural pollutant sources of dissolved and

suspended solids are exemplified by erosive soils that occur in western South Dakota

badlands and within the Missouri River basin (including considerable exposed marine

shale formations) and in extreme southeastern South Dakota (including large areas of

highly erodible loess soils). Large storm events that produce significant amounts of

precipitation may contribute to suspended sediment problems over large areas of the

state, particularly in the west and southeast. Fecal coliform concentrations also increase

significantly during times of above normal rainfall. Appropriate best management

practices should be applied to treat the sources of these and other parameters whose effects

are likely to be masked during periods of low precipitation.

31

In addition to rivers and streams, South Dakota has 570 classified publicly owned lakes

and reservoirs totaling nearly 205,000 acres. The 570 waterbodies are listed in ARSD

Chapter 74:51:02 and classified for aquatic life and recreation beneficial uses. GF&P

presently manages 450 state lakes for recreational fishing.

Excluding the four mainstem reservoirs, an estimated 22% of the 570 lakes have been

assessed, accounting for 65% of the total lake acreage. An estimated 49% (49 lakes) of

the lake acreage was considered to support all assessed beneficial uses and 51% (75

lakes) did not support assessed beneficial uses. Eighteen lakes assessed during the 2006

reporting cycle had insufficient information to make support determinations for this

reporting cycle. Approximately 98% of nonsupporting uses for lakes can be attributed to

nonpoint sources. Most lakes in the state are characterized as eutrophic to hypereutrophic.

They tend to be shallow and turbid and are well supplied with dissolved salts, nutrients,

and organic matter from often sizeable watersheds of nutrient rich glacial soils that are

extensively developed for agriculture. Runoff, carrying sediment and nutrients from

agricultural land, is the major nonpoint pollution source.

The mileage/acreage of use support for assessed surface waters in South Dakota during

this reporting cycle is summarized in Tables 8 through 13.

32

Type of Waterbody: Rivers and Streams (miles)

Degree of Use Assessment Basis

Support Evaluated Monitored

Total Assessed

Miles Fully

Supporting

- 3,906 3,906

Miles Insufficient

Data but Threatened

- - -

Miles Not

Supporting

- 3,998 3,998

TOTAL - 7,904 7,904

Type of Waterbody: Lakes and Reservoirs (acres)

Degree of Use Assessment Basis

Support Evaluated Monitored

Total Assessed

Acres Fully

Supporting

- 65,851 65,851

Acres Insufficient

Data but Threatened

4,012 - 4,012

Acres Not

Supporting

- 63,818 63,818

this report cycle. Waterbodies marked as “Threatened” in Tables 17 – 30 are placed in

Category 5, thus nonsupporting.

33

700 346 - - 1,046

1,461 1,759 - - 3,220

assessed)

1,611

2,295

assessed)

6,348

assessed)

7,870

assessed)

7,877

34

158 5 - - 163

26,677 10,109 375

37,161

3,089 18,308 -

21,397

48,974

assessed)

96,654 4,890 -

101,544

info)

123,559 55 8,421

132,035