Prepared in cooperation with the Bureau of Reclamation

Modeling the Water-Quality Effects of Changes to the 

Klamath River Upstream of Keno Dam, Oregon

U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2013–5135
Cover: Photograph showing the Klamath River near Keno, Oregon, looking 

downstream. (Photograph by Bureau of Reclamation field crew, January 17, 

2007.)
Modeling the Water-Quality Effects of 

Changes to the Klamath River Upstream of 

Keno Dam, Oregon

By Annett B. Sullivan, U.S. Geological Survey; I. Ertugrul Sogutlugil, Watercourse 

Engineering, Inc.; Stewart A. Rounds, U.S. Geological Survey; and Michael L. Deas, 

Watercourse Engineering, Inc.

Prepared in cooperation with the Bureau of Reclamation

Scientific Investigations Report 2013–5135

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director 

U.S. Geological Survey, Reston, Virginia: 2013

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Suggested citation:

Sullivan, A.B., Sogutlugil, I.E., Rounds, S.A., and Deas, M.L., 2013, Modeling the water-quality effects of changes to 

the Klamath River upstream of Keno Dam, Oregon: U.S. Geological Survey Scientific Investigations Report 2013–5135, 

60 p., http://pubs.usgs.gov/sir/2013/5135.
iii

Contents

Significant Findings .......................................................................................................................................1

Introduction.....................................................................................................................................................3

Model Background...............................................................................................................................3

Purpose and Scope ..............................................................................................................................6

Model Scenarios............................................................................................................................................8

Scenarios 1 and 2. Water-Quality Conditions Before and After TMDL Implementation...........8

Methods.........................................................................................................................................8

Results ...........................................................................................................................................8

Scenario 3. Compliance with Dissolved Oxygen, pH, and Ammonia Toxicity Criteria.............10

Water Quality Criteria................................................................................................................10

Dissolved Oxygen .............................................................................................................10

pH.........................................................................................................................................11

Ammonia Toxicity..............................................................................................................11

Natural Conditions Effect on Criteria.............................................................................12

Results .........................................................................................................................................12

Comparison to Dissolved-Oxygen Criteria....................................................................12

Comparison to pH Criteria ...............................................................................................15

Comparison to Ammonia Toxicity Criteria.....................................................................18

Scenario 4. Compare USGS Model and TMDL Model Results....................................................21

Methods.......................................................................................................................................21

Results .........................................................................................................................................21

Scenario 5. Particulate Matter Shunting ........................................................................................22

Methods.......................................................................................................................................22

Results .........................................................................................................................................22

Scenario 6. Decrease Particulate Organic Matter and Blue-Green Algae in Link River........23

Methods.......................................................................................................................................23

Results .........................................................................................................................................25

Scenario 7. Route Klamath River Water Through Treatment Wetlands ....................................27

Methods.......................................................................................................................................27

Wetland Locations............................................................................................................27

Wetland Effects on Water Quality..................................................................................29

Flow .....................................................................................................................................30

Results .........................................................................................................................................31

Scenario 8. Altered Flow—Import/Export to and from the Klamath Project ............................32

Methods.......................................................................................................................................32

Results .........................................................................................................................................32

Scenario 9. Augment Dissolved Oxygen or Add Riparian Shade ...............................................34

Methods.......................................................................................................................................34

Dissolved-Oxygen Augmentation...................................................................................34

Riparian Shade..................................................................................................................34

Results .........................................................................................................................................35

Dissolved-Oxygen Augmentation...................................................................................35

Shading...............................................................................................................................35
iv

Model Scenarios

Scenario 10. Climate Change Effects on Water Quality ...............................................................36

Methods.......................................................................................................................................36

Flows ................................................................................................................................36

Meteorological Conditions..............................................................................................37

Water Quality.....................................................................................................................38

Results .........................................................................................................................................39

Overview of Scenario Results....................................................................................................................40

Future Application and Development.......................................................................................................41

Acknowledgments.......................................................................................................................................42

Supplementary Materials...........................................................................................................................42

References Cited..........................................................................................................................................42

Appendix A. Volume-Average Annual and June–October Scenario Results for the 

Link-Keno Reach, Upper Klamath River, Oregon.......................................................................45

Contents—Continued

Figures

1. Map showing location of the Link River to Keno Dam reach of the Klamath River,

Oregon ............................................................................................................................................4

2. Graphs showing components of total phosphorus and total nitrogen loads for Link

River, Oregon, during model year 2007......................................................................................5

3. Schematic diagram of model segments in the main branch of the Link-Keno

model, Klamath River, Oregon ....................................................................................................7

4. Graph showing simulated dissolved-oxygen concentration under the base case

and for scenarios 1b, 2a, 2b in the Link-Keno reach, Klamath River, Oregon, on

August 1, 2007..............................................................................................................................10

5. Graphs showing dissolved-oxygen concentrations for the base case scenario

(3[1a]) and reference conditions (3[nc]) scenarios, and hourly, 7-, and 30-day

dissolved-oxygen criteria for the upper Klamath River at Miller Island (model

segment 38), Oregon, 2007 ........................................................................................................14

6. Graphs showing pH and ammonia concentrations from scenario [3(2a)], and

criteria for pH and acute and chronic ammonia toxicity for the upper Klamath

River at Miller Island (model segment 38), Oregon, 2007.....................................................16

7. Graphs showing comparison of measured daily average pH with daily average

model results from the calibrated USGS model and scenario 4 TMDL model for

sites in the Link-Keno reach of the Klamath River, Oregon, 2007 .......................................21

8. Graph showing simulated dissolved-oxygen concentration under the base case

and for scenario 5 in the Link-Keno reach of the Klamath River, Oregon, 

August 1, 2007..............................................................................................................................22
v

9. Graphs showing simulated water-quality conditions at 1 meter depth at Keno

(model segment 95) for the base case and for scenario 6 model simulations of 90

percent decrease of particulate organic matter (POM) and blue-green algae at

Link River, Oregon.......................................................................................................................26

10. Graph showing simulated dissolved-oxygen concentration in the Link-Keno

reach, Klamath River, Oregon on August 1, 2007 under the base case and for

scenario 6 decreases in Link River algae and particulate organic matter.......................27

11. Graph showing relation between Link River particulate organic matter and algae

load decrease and the predicted dissolved oxygen increase in the Link-Keno

reach, Klamath River, Oregon, for each of the years modeled, 2006–09...........................27

12. Schematic diagram showing the CE-QUAL-W2 model grid, location of wetland A

and B areas, and approximate diversion and return flow points for scenario 7

simulations, Klamath River, Oregon.........................................................................................28

13. Graphs showing simulated dissolved-oxygen concentration under the base case

and for wetland simulations in scenario 7 in the Link-Keno reach of the Klamath

River, Oregon, August 1, 2007 ...................................................................................................31

14. Graph showing simulated dissolved-oxygen concentration under the base case

and for flow routing simulations in scenario 8 in the Link-Keno reach of the

Klamath River, Oregon, August 1, 2007....................................................................................33

15. Graphs showing simulated daily average flow, velocity, total dissolved solids, and

dissolved oxygen at segment 8 for the base case (scenario 1a) and scenario 8b,

Klamath River, Oregon, 2007 .....................................................................................................33

16. Graph showing simulated dissolved-oxygen concentration under the base case

and for saturated and supersaturated model runs for scenario 9 in the Link-Keno

reach of the Klamath River, Oregon, August 1, 2007.............................................................35

17. Graph showing simulated water temperature under the base case and for

shading simulations in scenario 9 in the Link-Keno reach of the Klamath River,

Oregon, August 1, 2007 ..............................................................................................................36

18. Graph showing outflows from the CE-QUAL-W2 base-case model for 2006–09 and

from the Canadian Centre for Climate Modeling Analysis (CCCMA) model for

2012–60 at Keno Dam, Klamath River, Oregon .......................................................................37

19. Graph showing annual average outflow at Keno Dam, Klamath River, Oregon...............37

20. Graphs showing measured weekly mean water temperature versus measured

weekly mean air temperature, with the final fitted equation for the entire

simulation period (2006–09) for Link River, Lost River Diversion Channel, Klamath

Straits Drain, Klamath River, Oregon.......................................................................................39

21. Graph showing simulated water temperature under the base case and climate

warming simulations in scenario 10 for the Link-Keno reach of the Klamath River,

Oregon, August 1, 2007 ..............................................................................................................39

22. Graphs showing simulated water quality for scenarios 1, 2, 5, 6, 7, 8, 9 and 10 for

the Link-Keno reach of the Klamath River, Oregon...............................................................40

Figures—Continued
vi

Tables

1. Total phosphorus and total nitrogen loads for upstream inflow, point, and

nonpoint sources in the Link-Keno reach base case model, Klamath River,

Oregon, 2006–09............................................................................................................................5

2. Summary of model scenarios for the Link-Keno Reach, Klamath River, Oregon ..............9

3. Number of days dissolved oxygen was simulated to be less than the 30-day

criteria (and the average amount less than the criteria) at selected Oregon

Department of Environmental Quality compliance locations for scenario 3 under

the base case and Total Maximum Daily Load scenarios, Klamath River, Oregon,

for years 2006–09 ........................................................................................................................13

4. Number of days pH was simulated to be greater than the 9.0 criteria (and the

average amount greater than the criteria) at selected Oregon Department of

Environmental Quality compliance locations for scenario 3 under the base case

and Total Maximum Daily Load scenarios, Klamath River, Oregon, for years 2006–09...15

5. Number of days acute ammonia toxicity was greater than the criteria (and

average amount greater than the criteria) at selected Oregon Department of

Environmental Quality compliance locations for scenario 3 under the base case

and Total Maximum Daily Load scenarios, Klamath River, Oregon, for years 2006–09...19

6. Number of days chronic ammonia toxicity was greater than criteria (and average

amount greater than the criteria) at selected Oregon Department of

Environmental Quality compliance locations for scenario 3 under the base case

and Total Maximum Daily Load scenarios, Klamath River, Oregon, for years 2006–09...20

7. Annual particulate organic material and algae load decreases for scenario 6,

Link-Keno reach of the Klamath River, Oregon, 2006–09 .....................................................23

8. Particulate organic material and algae load decreases (June 15–October 31) for

scenario 6, Link-Keno reach of the Klamath River, Oregon, 2006–09.................................24

9. Wetland representations for scenario 7 simulations, Klamath River, Oregon .................27

10. Wetland calculator results (required wetland area and removal rates) for model

segments 28 and 54 of the Link-Keno reach for influent maximum, average, and

minimum biochemical oxygen demand and total suspended solids per 100 cubic

feet per second of flow diverted to a wetland in the Link-Keno reach of the

Klamath River, Oregon ...............................................................................................................29

11. Specified decreases in modeled return flow due to removals of biochemical

oxygen demand, total suspended sediment, total nitrogen, and total phosphorus

through treatment wetlands for scenario 7 in the Link-Keno reach of the Klamath

River, Oregon ...............................................................................................................................30

12. Flow rates used in scenario 8, Klamath River, Oregon.........................................................32

13. Annual average change in air temperature between 2006–09 and 2057–60 from

five Global Circulation Models for the Klamath River basin, Oregon.................................37

14. Final parameter estimates of the non-linear regression model for major inputs at

selected sites in the Link-Keno reach of the Klamath River, Oregon, 2006–09 ................38
vii

Conversion Factors, Datums, and Abbreviations and 

Acronyms

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

acre 0.4047 hectare (ha)

foot (ft) 0.3048 meter (m)

foot per second (ft/s) 0.3048 meter per second (m/s)

mile (mi) 1.609 kilometer (km)

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

SI to Inch/Pound

Multiply By To obtain

kilogram (kg) 2.205 pound avoirdupois (lb)

meter (m) 3.281 foot (ft) 

metric ton 1.102 ton (ton) 

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F=(1.8×°C)+32.

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L), 

which is approximately equivalent to parts per million (ppm), or micrograms per liter (μg/L), 

which is approximately equivalent to parts per billion (ppb).

Datums

Elevation refers to distance above the vertical datum. A local vertical datum, Upper Klamath 

Lake Vertical Datum (UKLVD) is used, which was established by the Bureau of Reclamation. For 

the purpose of this report, the conversion is UKLVD – 1.78 ft = National Geodetic Vertical Datum 

of 1929 (NGVD 29).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).
viii

Abbreviations and Acronyms

BOD biochemical oxygen demand

BOD5 5-day biochemical oxygen demand

EPA U.S. Environmental Protection Agency

GCM Global Circulation Model

ISS inorganic suspended sediment

LDOM labile dissolved organic matter

LPOM labile particulate organic matter

NH3 un-ionized ammonia

NH4 shorthand for ammonia plus ammonium in this report

NH4

+ ammonium

NO3 shorthand for nitrate in this report

ODEQ Oregon Department of Environmental Quality

PO4 shorthand for orthophosphorus in this report

RDOM refractory dissolved organic matter

RPOM refractory particulate organic matter

T water temperature

TIC total inorganic carbon

TMDL Total Maximum Daily Load

TN total nitrogen

TP total phosphorus

TSS total suspended solids

USGS U.S. Geological Survey

Conversion Factors, Datums, and Abbreviations and 

Acronyms—Continued
Modeling the Water-Quality Effects of Changes to the 

Klamath River Upstream of Keno Dam, Oregon

By Annett B. Sullivan1, I. Ertugrul Sogutlugil2, Stewart A. Rounds1, and Michael L. Deas2

Significant Findings

The Link River to Keno Dam (Link-Keno) reach of the 

Klamath River, Oregon, generally has periods of water-quality 

impairment during summer, including low dissolved oxygen, 

elevated concentrations of ammonia and algae, and high pH. 

Efforts are underway to improve water quality in this reach 

through a Total Maximum Daily Load (TMDL) program 

and other management and operational actions. To assist in 

planning, a hydrodynamic and water-quality model was used 

in this study to provide insight about how various actions 

could affect water quality in the reach. These model scenarios 

used a previously developed and calibrated CE-QUAL-W2 

model of the Link-Keno reach developed by the U.S. 

Geological Survey (USGS), Watercourse Engineering Inc., 

and the Bureau of Reclamation for calendar years 2006–09 

(referred to as the “USGS model” in this report). Another 

model of the same river reach was previously developed by 

Tetra Tech, Inc. and the Oregon Department of Environmental 

Quality for years 2000 and 2002 and was used in the TMDL 

process; that model is referred to as the “TMDL model” in 

this report.

This report includes scenarios that (1) assess the 

effect of TMDL allocations on water quality, (2) provide 

insight on certain aspects of the TMDL model, (3) assess 

various methods to improve water quality in this reach, 

and (4) examine possible water-quality effects of a future 

warmer climate. Results presented in this report for the first 

5 scenarios supersede or augment those that were previously 

published (scenarios 1 and 2 in Sullivan and others [2011], 

3 through 5 in Sullivan and others [2012]); those previous 

results are still valid, but the results for those scenarios in this 

report are more current.

Significant findings from this study include:

• When comparing two sets of potential water-quality 

improvements, one in which Upper Klamath Lake 

attained its TMDL target and another in which 

Klamath River point and nonpoint sources between 

Link and Keno Dams met TMDL allocations, it 

was found that the first had a larger beneficial effect 

on Link-Keno reach water quality compared to 

the second. For example, June to October average 

dissolved-oxygen concentrations increased 2.4–

3.6 mg/L (54–126 percent), depending on the year, 

when the upstream inflow from Upper Klamath 

Lake was simulated at its TMDL target. In contrast, 

when Klamath River point and nonpoint sources 

met TMDL allocations, June to October average 

dissolved-oxygen concentrations increased by 

0.1–0.24 mg/L (2–4 percent). This comparison was 

similar for most water-quality constituents, although 

both sets of improvements had notable effects on 

decreasing orthophosphorus concentrations in the 

Link- Keno reach.

• Under base case conditions 2006–09, digressions less 

than the State of Oregon dissolved-oxygen criteria 

occurred most frequently in summer in the Link-Keno 

reach. Considering the three dissolved-oxygen criteria 

that must be met, the 30-day criteria were most 

difficult to attain. The dissolved-oxygen criteria were 

met for the longest period in the upstream reach nearer 

Link River, with non-attainment periods increasing in 

the downstream direction toward Keno Dam, due in 

part to the decay of algae and organic matter through 

the reach.

• Simulations with Upper Klamath Lake at its TMDL 

water quality target overall were more effective at 

reducing the number of days when dissolved-oxygen 

criteria were not met, compared to simulations in 

which Klamath River point and nonpoint sources were 

assumed to meet the Klamath River TMDL allocations. 

1

U.S. Geologial Survey

2

Watercourse Engineering, Inc.
2 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Setting the point and nonpoint sources at TMDL 

allocations was predicted to help meet the dissolvedoxygen criteria when Upper Klamath Lake also was at 

its TMDL target.

• Under base case conditions, the Link-Keno reach 

exceeded the State of Oregon maximum pH criterion 

of 9.0 in summer at certain times and locations, 

especially in areas where algal blooms were present. 

Algal populations were greatest in the upstream 

portion of the reach, which led to more frequent pH 

criterion exceedances in that part of the river.

• Although the TMDLs addressed factors such as total 

nitrogen, total phosphorus, and biochemical oxygen 

demand (BOD) for inflows and point and nonpoint 

sources, other water-quality constituents such as pH 

and total inorganic carbon (TIC) likely would change 

as TMDL responses are implemented, but it is more 

difficult to predict these future levels because they 

are affected by watershed conditions that lie outside 

the Link-Keno model domain. Simulations of Upper 

Klamath Lake and Link-Keno sources at TMDL 

targets and allocations indicated that Link-Keno 

model pH predictions were sensitive to boundary and 

point and nonpoint source estimates of pH and total 

inorganic carbon.

• Under base case conditions, the acute ammonia 

toxicity criteria were simulated to be exceeded from 

0 to 27 days per year, depending on location and 

year. The chronic ammonia toxicity criteria were 

simulated to be exceeded more frequently, between 11 

and 158 days per year. Because the ammonia criteria 

are pH-dependent, these criteria were sensitive to 

the formulation of pH and TIC in the boundaries of 

model scenarios.

• A qualitative comparison of the USGS and TMDL 

model pH simulations indicated that the USGS model 

more closely simulated the measured seasonal patterns 

in pH for years 2006-09. This is due in part to (1) the 

enhanced buffering capabilities added to the USGS 

model, which includes pH buffering by organic matter, 

orthophosphorus, and ammonia and (2) the inclusion 

of macrophytes in the USGS model.

• Shunting, or diverting, particulate matter so that 

it remained in the Klamath River instead of being 

removed through four Klamath Project diversion 

canals, was predicted to worsen water quality in 

the Link-Keno reach as measured by the predicted 

concentrations of dissolved oxygen, ammonia, and 

chlorophyll a.

• Model results indicated that removal of large algae 

and particulate organic matter at the Link River inflow 

could improve water quality in the Link-Keno reach, 

greatly increasing dissolved oxygen and decreasing 

nutrients and chlorophyll a. However, the downstream 

pH may remain high in summer. Removing material 

for the entire year had only a small additional benefit 

compared to treatment for the primary growth period 

of June–October. A significant fraction of the algae 

and particulate material would need to be removed 

to bring the river closer to compliance with the 

dissolved-oxygen criteria.

• Routing river water through wetlands adjacent 

to the Klamath River was simulated to remove 

particulate inorganic and organic matter, algae, 

and labile dissolved organic matter from the river 

water, leading to increases in dissolved oxygen and 

decreases in nutrient, organic matter, and chlorophyll a

concentrations downstream of the wetland. Wetlands 

farther upstream in the Link-Keno reach are potentially 

more advantageous, as they could treat the higher 

levels of particulate material and algae found there.

• Reducing Link River flows by 200 ft3/s and routing 

that water through the Klamath Project and back to 

the Klamath River through the Lost River Diversion 

Channel, the Klamath Straits Drain, or both was 

predicted to have only modest effects on water quality 

in the Link-Keno reach, with some improvements and 

some degradation depending on location and time 

of year.

• Scenarios that examined the effects of reaeration 

and dissolved-oxygen injection revealed that these 

treatments are likely to be effective at increasing 

dissolved-oxygen concentrations in the reach, 

although it was predicted that such actions would 

have negligible short-term effects on other waterquality constituents.

• In scenarios that focused on reducing concentrations of 

particulate organic matter or algae, the point of greatest 

improvement in dissolved oxygen was typically farther 

downstream of the treatment location, and may even 

be downstream of the lower boundary of the model 

at Keno Dam. In contrast, in a scenario that directly 

injected dissolved oxygen, the point of greatest 

improvement was immediately downstream of the 

treatment location.
Introduction 3

• Simulations of increased riparian shade along the LinkKeno reach produced cooling of less than 0.6°C as a 

reach average for June–October. Less solar radiation 

reaching the river also led to minor effects on other 

water-quality constituents that are affected by water 

temperature and photosynthesis.

• Simulations of a future warmer climate with 

air temperature increases of 0.86–3.25°C were 

predicted to increase annual average water 

temperatures by 0.6–2.4°C in the Link-Keno reach. 

Warmer temperatures would lead to lower dissolved 

oxygen solubility and the simulations predicted 

dissolved-oxygen concentration decreases on the order 

of 0.3 mg/L as an annual average with the maximum 

air temperature increase of 3.25°C.

Results from these model scenarios demonstrate that 

large changes in river water quality can be achieved through 

one or more management strategies that target the most 

important inputs and (or) instream water-quality processes 

of the upper Klamath River. Future tests and refinements 

of the model based on research, targeted monitoring, and 

pilot studies of potential management actions are likely 

to further improve the accuracy and value of these model 

predictions. As potential management plans are refined, the 

model can be used to provide further insights about likely 

water-quality outcomes.

Introduction

The Klamath River flows about 255 mi (410 km) from 

the outlet of Upper Klamath Lake through southern Oregon 

and northern California to the Pacific Ocean. The first 20 mi 

of the river, just downstream of Upper Klamath Lake, are 

bounded by Link River and Keno Dam (fig. 1). Water quality 

in this reach has been classified as “very poor” by the State of 

Oregon (Mrazik, 2007) and was designated as “water quality 

limited” for exceeding ammonia toxicity and dissolvedoxygen criteria year-round, and pH and the chlorophyll a

criterion in summer (Oregon Department of Environmental 

Quality, 2007). A Total Maximum Daily Load (TMDL) for 

the Klamath River including this reach (Oregon Department 

of Environmental Quality, 2010) was approved by the 

Environmental Protection Agency in May 2012. The TMDL 

specifies load decreases of total nitrogen, total phosphorus, 

and 5-day biochemical oxygen demand (BOD5) for the 

nonpoint sources Lost River Diversion Channel and Klamath 

Straits Drain and for point sources including the Klamath 

Falls and South Suburban wastewater treatment plants. At 

the time of this study, the temperature section of the upper 

Klamath River TMDL was not approved and was undergoing 

additional analysis. 

Most nutrient loads in the Link River to Keno Dam 

(Link-Keno) reach came from Upper Klamath Lake through 

Link River with additional input by nonpoint and point sources 

in the Link-Keno reach (table 1). Total phosphorus loads 

in Link River consisted of phosphorus in algae, particulate 

organic matter, dissolved organic matter, and orthophosphorus. 

Total nitrogen loads in Link River were comprised of algae, 

particulate organic matter, dissolved organic matter, nitrate, 

and ammonia. The relative contribution of those various 

nutrient sources varied through the year (fig. 2).

A TMDL for Upper Klamath Lake, just upstream of 

the study reach was approved by the U.S. Environmental 

Protection Agency in 2002. That TMDL specifies decreases 

in inflow loads and provides an in-lake phosphorus target 

(Oregon Department of Environmental Quality, 2002). 

Changes of water quality in Upper Klamath Lake would affect 

water quality in Link River, the upstream boundary of the 

Link-Keno model.

In addition to TMDL actions, other management options 

are being considered that may improve water quality in the 

Link-Keno reach. Running scenarios based on a calibrated 

water-quality model of the reach allows the effects of 

such options to be predicted and fully considered so that 

management and restoration efforts can focus on strategies 

with the highest likelihood of success. Only the water-quality 

effects of potential management actions are discussed here; 

other aspects of water-quality improvement options, such 

as cost or implementation timeframes, are not included in 

this report.

Model Background

River water quality can be affected by hydrology, weather 

and climate atmospheric conditions, inputs and withdrawals, 

chemical reactions, and biota. Mechanistic computer models 

such as CE-QUAL-W2 (Cole and Wells, 2008) include many 

of these processes and are regularly used to make predictions 

about the potential water quality response to system changes. 

Models commonly are used in constructing TMDLs, and the 

upper Klamath River TMDL was based in part on results from 

a CE-QUAL-W2 model that used conditions from years 2000 

and 2002 (Rounds and Sullivan, 2009; Tetra Tech, Inc., 2009; 

Rounds and Sullivan, 2013). That model from Tetra Tech, 

Inc. and the Oregon Department of Environmental Quality 

(ODEQ) is referred to as the “TMDL model” in this report.
4 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

tac13-0843_fig 01

Ady Canal

West Canal 

A

Canal

Canal

Canal

North

Klamath

Klamath

Strait

River

Wocus

Drainage

Lake

Ewauna

Spring

Lake

UPPER

KLAMATH

LAKE

Round

Lake

140

140

140

39

39

39

66

66

97

97

420451121510000 Sampling site

EXPLANATION

Upper

Klamath

Basin

OREGON

CALIFORNIA

Wocus

Pelican

City

Midland

Keno

Klamath

Falls

Keno 

Dam

Altamont

Keno

11509370

Keno

Outflow

KRS 12a

420615121533600

Link River

11507501

Link River

11507500

Pelican

Marina

Klamath Falls

WWTP

Columbia

Forest

Products

South Suburban

WWTP

Miller Island

420853121505500

Railroad Bridge

421209121463000

Klamath Straits Drain

420451121510000

Lost River 

Diversion Channel

421015121471800

Link River

Dam

121°55' 121°50' 121°45'

42°

15'

42°

10'

42°

05'

0 1 2 3 4 5 MILES

0 1 2 3 4 5 KILOMETERS

Figure 1. Location of the Link River to Keno Dam reach of the Klamath River, Oregon. (WWTP, wastewater treatment plant.)
Introduction 5

Table 1. Total phosphorus and total nitrogen loads for upstream inflow, point, and nonpoint sources in the 

Link-Keno reach base case model, Klamath River, Oregon, 2006–09. 

Site name Site type Total phosphorus (metric tons per calendar year)

2006 2007 2008 2009

Link River Upstream inflow 188 128 128 114

Klamath Falls wastewater treatment plant Point source 13 11 11 8

South Suburban wastewater treatment plant Point source 11 10 9 8

Lost River Diversion Channel Nonpoint source 66 17 19 10

Columbia Forest Products Point source 0.003 0.001 0.000 0.000

Klamath Straits Drain Nonpoint source 76 31 32 30

Site name Site type Total nitrogen (metric tons per calendar year)

2006 2007 2008 2009

Link River Upstream inflow 2,488 1,819 1,948 1,746

Klamath Falls wastewater treatment plant Point source 65 54 53 49

South Suburban wastewater treatment plant Point source 43 39 36 33

Lost River Diversion Channel Nonpoint source 617 142 158 70

Columbia Forest Products Point source 0.038 0.009 0.003 0.001

Klamath Straits Drain Nonpoint source 506 285 319 278

Jan. Feb. Mar. Apr. May June July Aug. Sept. Oct. Nov. Dec.

2007

0

10

20

30

40

A. Phosphorus load

0

100

200

300

400

500

B. Nitrogen load

Phosphorus load,

in kilograms per hour

Nitrogen load,

in kilograms per hour

EXPLANATION

PO4

DOM

POM

Algae

NH4

NO3

Figure 2. Components of total phosphorus and total nitrogen 

loads for Link River, Oregon, during model year 2007. Total 

phosphorus consists of phosphorus in algae, particulate 

organic matter (POM), dissolved organic matter (DOM), and 

orthophosphate (PO4

). Total nitrogen consists of nitrogen in 

algae, POM, DOM, nitrate (NO3

), and ammonia (NH4). Values are 

weekly moving averages of hourly model input.
6 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

In an effort to improve the understanding of instream 

processes in this river reach and create a more accurate 

predictive model, the U.S. Geological Survey (USGS), 

Watercourse Engineering Inc. (Watercourse), and Bureau 

of Reclamation (Reclamation) collaborated in a research, 

monitoring, and modeling study that produced a calibrated 

CE-QUAL-W2 version 3.6 model of the Link-Keno reach 

for conditions during 2006-09 (Sullivan and others, 2011). 

This new model was based on extensive field data, with 

additional field research on issues of flow, suspended matter 

settling, and dissolved oxygen and organic matter dynamics 

(Sullivan and others, 2008, 2009, 2010; Poulson and Sullivan, 

2010; Deas and Vaughn, 2011) to better define model 

parameters and rates. Subsequently, this calibrated model 

was updated to include macrophytes and improvements to 

the simulation of pH (Sullivan and others, 2013). This 

USGS-Watercourse-Reclamation model (referred to as the 

“USGS model”) can simulate stage, flow, water velocity, ice 

cover, water temperature, specific conductance, inorganic 

suspended sediment, total nitrogen, particulate nitrogen, 

nitrate, ammonia, total phosphorus, orthophosphorus, 

particulate carbon, dissolved organic carbon, organic matter 

in the sediment, three algal groups, three macrophyte groups, 

dissolved oxygen, and pH.

CE-QUAL-W2 is a two-dimensional model, simulating 

variability from upstream to downstream and from the river 

surface to the channel bottom. The third dimension, from bank 

to bank, is laterally averaged. As such, the model is well suited 

for the simulation of conditions in long, narrow waterbodies 

such as rivers and reservoirs that tend to stratify thermally; 

in such waterbodies, the vertical variability of water quality 

tends to be more distinct than any lateral variability. The main 

branch of the Link-Keno model grid consists of 102 segments 

that connect together in the direction of flow (fig. 3); segments 

average 1,009 ft (308 m) in length. Each segment represents 

a cross-sectional shape of the river channel, with stacked 

layers of varying width from the river surface to the channel 

bottom. A side view of the model grid is available in Sullivan 

and others (2011). Vertical layers in the USGS model grid 

were 0.61 m in height. The model keeps track of all simulated 

constituents in all layers of every segment, and can output 

results at selected locations and time intervals, often hourly.

Although the Link-Keno model was constructed and 

calibrated for conditions in the years 2006-09, the mechanistic 

nature of the models allows for useful predictions of 

hydrodynamic, thermal, and water-quality changes resulting 

from altered conditions. However, all model predictions have 

some uncertainty. Results from model scenario runs are most 

useful in providing insights regarding changes to the system 

through comparative analysis, rather than in providing high 

certainty regarding the values of predicted concentrations. For 

example, scenario results can be used to evaluate decisions 

about which treatment or restoration processes might be most 

effective at improving water quality by assessing the predicted 

changes in key constituent concentrations.

These scenarios were developed by the USGS and 

Watercourse in cooperation with Reclamation. Scenario 

results will inform local and regional managers who need 

information about potential approaches to improve waterquality conditions while efficiently managing the system for 

multiple uses.

Purpose and Scope

The purpose of this study was to predict the potential 

water-quality effects of management strategies and other 

system changes through the application of the USGS model 

of the upper Klamath River from the mouth of Link River to 

Keno Dam. Most model scenarios were superimposed on the 

wide range of conditions that occurred for the years 2006-09, 

thus allowing simulation of a range of climatic, hydrologic, 

and water-quality conditions. These model scenarios were 

formulated and run to:

1. Assess the effect of TMDL total phosphorus, total 

nitrogen, and BOD5 targets and allocations on upper 

Klamath River water quality (scenarios 1-2), and compare 

those results to the relevant Oregon dissolved oxygen, pH, 

and ammonia toxicity criteria (scenario 3);

2. Evaluate the importance of differences in the formulations 

of the USGS and TMDL models (scenario 4);

3. Assess various water quality improvement options 

related to particulate material, wetland treatment, flow 

management, shading, and oxygen injection (scenarios 5, 

6, 7, 8, 9);

4. Examine the possible effects of a warmer climate on river 

water quality (scenario 10).

Preliminary results from model scenarios 1 through 5 

were published previously (Sullivan and others, 2011, 2012). 

The results presented in this report expand upon or augment 

those results; the previous results are still valid, although the 

results in this report are more current.
Introduction 7

tac13-0843_fig 03

2

80

40

60

100

20

Keno Dam

Link River

Figure 3. Model segments in the main branch of the Link-Keno model, Klamath River, Oregon. The first 

segment downstream of Link River is model segment 2 and the last model segment, at Keno Dam, is 

model segment 103. Segment widths vary according to river width.
8 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Model Scenarios

To assess changes in water quality, scenario-specific 

results were compared to results from the base case (current 

conditions) model documented in Sullivan and others 

(2013) for calendar years 2006–09. After each scenario was 

constructed and run, the model water-surface elevation at 

Keno Dam was assessed to ensure that it was unchanged 

from the base case model. This allowed base case and model 

scenario results to be directly compared without confounding 

traveltime or storage effects from water stage differences. 

Some of the scenarios that examine treatment options are 

exploratory in nature and include end member cases, to 

examine the range of possible effects. Methodology and 

results from all scenarios (table 2) are discussed in this report 

in numerical order.

Scenarios 1 and 2. Water-Quality Conditions 

Before and After TMDL Implementation

The Klamath River TMDL specifies total nitrogen, total 

phosphorus, and BOD5 allocations for point and nonpoint 

tributary sources along the Link-Keno reach. The Upper 

Klamath Lake TMDL specifies an in-lake total phosphorus 

target; the water quality of Upper Klamath Lake affects the 

Klamath River’s upstream inflow at Link River. Scenarios 1 

and 2 were formulated to assess the water-quality changes in 

the upper Klamath River if the upper Klamath River TMDL 

tributary source allocations and Upper Klamath Lake TMDL 

target were met, both separately (scenarios 1b, 2a) and 

together (scenario 2b) (table 2).

Methods

Methods to construct scenarios 1 and 2 were described 

in Sullivan and others (2011). The model runs in this study 

were similar, but used updated and recalibrated USGS models, 

which included macrophytes and enhanced pH-buffering 

calculations (Sullivan and others, 2013) that were not 

included in the previous USGS model runs (Sullivan and 

others, 2011). Because the new pH buffering algorithms 

apportion some alkalinity to organic matter, ammonia, and 

orthophosphorus, recalculation of the total inorganic carbon 

(TIC) concentrations in the boundary input files was necessary 

(see Sullivan and others, 2013). This TIC recalculation applied 

to all boundary inputs, including Link River, point sources 

(Klamath Falls and South Suburban wastewater treatment 

plants) and nonpoint sources (Lost River Diversion Channel, 

Klamath Straits Drain).

In addition to recalculating TIC for base case conditions, 

inflow TIC for the upstream and point and nonpoint sources 

was recalculated for scenarios in which inflow concentrations 

of organic matter, ammonia, and (or) orthophosphorus 

were decreased to be consistent with TMDL allocations. If 

concentrations of nutrients, organic matter, and (or) algae 

were decreased in the inflows by changes that affected the 

watershed ecosystem of those sources, the pH of those waters 

could have changed as well; pH affects the calculation of 

TIC. Predicting pH changes that might occur outside the 

model boundary is more difficult, so some sensitivity analyses 

explored the ramifications of boundary pH changes during 

2007. For this bracketing, TIC was calculated twice: first using 

measured pH and second using an estimated pH that might 

have occurred in the presence of a smaller algal population 

(low-bloom condition). Considering winter background pH 

of inflows (pH approximately 7.0–8.0) with some minor 

primary production in summer, might lead to maximum pH 

values of approximately 8.5. Thus, the low-bloom pH was 

estimated by setting any inflow pH values greater than 8.5 to 

8.5. Under the base case, current conditions, the measured pH 

for some inputs were greater than 9.5 for some periods during 

the year. Separate model runs were conducted for each of 

these conditions.

Results

Scenario 1 and 2 results from the updated model were 

similar to scenario results from the original model as discussed 

in Sullivan and others (2011). Inflow nutrient decreases 

in Link River (to meet the Upper Klamath Lake TMDL 

target) and in the two wastewater treatment plants, Lost 

River Diversion Channel and Klamath Straits Drain (to meet 

Klamath River TMDL allocations) together (scenario 2b) 

were effective at improving water quality in the Link-Keno 

reach of the upper Klamath River, as measured by increased 

dissolved-oxygen concentrations, decreased ammonia 

concentrations, and improvements in other water-quality 

parameters (fig. 4; tables A1, A2).

The predicted improvement in water quality caused by 

the attainment of the Upper Klamath Lake TMDL target, 

as reflected by improved Link River inflow quality, was 

more than the improvement in water quality associated with 

the TMDL attainment of all other inflows combined. For 

instance, the Link-Keno volume-average dissolved-oxygen 

concentration for June through October was predicted to 

increase 2.4–3.6 mg/L (54–126 percent) depending on model 

year, when Link River water quality reflected attainment of 

the Upper Klamath Lake TMDL target (scenario 2a) compared 

to base case (scenario 1a) conditions (fig. 4; table A2). In 

contrast, the dissolved-oxygen concentration was predicted to 

increase by much less, 0.1–0.2 mg/L (2–4 percent), through 

the attainment of all Klamath River TMDL allocations at the 

two wastewater treatment plants, the Lost River Diversion 

Channel, and the Klamath Straits Drain (scenario 1b), 

compared to base case conditions.
Model Scenarios 9

Table 2. Summary of model scenarios for the Link-Keno Reach, Klamath River, Oregon. 

[Scenario 3 is based on further analyses of scenarios 1 and 2. Most scenarios were run for calendar years 2006–09; 

scenario 10 was run based on calendar year 2007. Abbreviations: TMDL, total maximum daily load; DO, dissolved 

oxygen; OM, organic matter; ft3/s, cubic foot per second; m, meter]

Scenario 

number Description

Scenario 1: Base case and sources at TMDL allocations

1a Base case (current conditions)

1b Sources at TMDL allocations

Scenario 2: Link River at Upper Klamath Lake TMDL target

2a Link River at Upper Klamath Lake TMDL target

2b Link River at Upper Klamath Lake TMDL target and sources at TMDL allocations

Scenario 3: Compliance with dissolved oxygen, pH, and ammonia toxicity criteria

3(nc) Reference conditions, without anthropogenic effect

3(1a) Base case (current conditions)

3(1b) Sources at TMDL allocations

3(2a) Link River at Upper Klamath Lake TMDL target

3(2b) Link River at Upper Klamath Lake TMDL target and sources at TMDL allocations

Scenario 4: Compare U.S. Geological Survey model and TMDL model results

4 Apply 2006–09 data to TMDL model

Scenario 5: Particulate matter shunting

5a Shunt, Lost River Diversion Channel and Klamath Straits Drain at current conditions

5b Shunt, Lost River Diversion Channel and Klamath Straits Drain at intermediate conditions

5c Shunt, Lost River Diversion Channel and Klamath Straits Drain at zero OM, nutrients, and 

algae, DO at saturation

Scenario 6: Decrease particulate organic matter and blue-green algae in Link River

6a 25 percent decrease, June 15–October 31

6b 50 percent decrease, June 15–October 31

6c 90 percent decrease, June 15–October 31

6d 25 percent decrease, entire year

6e 50 percent decrease, entire year

6f 90 percent decrease, entire year

Scenario 7: Route Klamath River water through treatment wetlands

7a Segment 28, 50 percent decrease, entire river

7b Segment 28, 50 percent decrease, 250 ft3

/s

7c Segment 28, 90 percent decrease, entire river

7d Segment 54, 50 percent decrease, entire river

7e Segment 54, 50 percent decrease, 250 ft3

/s

7f Segment 54, 90 percent decrease, entire river

Scenario 8: Altered flow: Import/export to/from the Klamath Project

8a Flow to Lost River Diversion Channel

8b Flow to Klamath Straits Drain

8c Flow to Lost River Diversion Channel and Klamath Straits Drain

Scenario 9: Augment dissolved oxygen or add riparian shade

9a DO saturation, segment 7 (Railroad Bridge)

9b DO saturation, segment 21 (Highway 97)

9c DO saturation, segment 38 (Miller Island)

9d DO supersaturation, segment 7 (Railroad Bridge)

9e DO supersaturation, segment 21 (Highway 97)

9f DO supersaturation, segment 38 (Miller Island)

9g Riparian shade, 10 m trees

9h Riparian shade, 20 m trees

Scenario 10: Climate change effects on water quality

10a Minimum future temperature increase

10b Median future temperature increase

10c Maximum future temperature increase
10 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Similarly, water quality improvements for ammonia, 

chlorophyll a, particulate organic carbon, dissolved organic 

carbon, total phosphorus, and total nitrogen were notably 

greater when Link River inputs reflected attainment of 

the Upper Klamath Lake TMDL target compared to when 

the other inflows met Klamath River TMDL allocations 

(tables A1, A2). Decreases in orthophosphorus concentration, 

on the other hand, were notable both when Link River 

reflected Upper Klamath Lake TMDL attainment (scenario 2a) 

and when the in-reach inflows met Klamath River TMDL 

allocations (scenario 1b): June–October orthophosphorus 

concentrations decreased 0.04–0.07 mg/L with the first 

condition and 0.02–0.03 mg/L under the second compared 

to base case conditions (scenario 1a) (table A2). Upper 

Klamath Lake inflows are a dominant factor in determining 

water quality in the Link-Keno reach of the Klamath River, 

particularly during summer. Other sources of water to the 

reach can be important in affecting certain constituents such 

as phosphorus, but significant changes to water quality in this 

reach are unlikely without alterations in the quality of Upper 

Klamath Lake inflows.

Scenario 3. Compliance with Dissolved Oxygen, 

pH, and Ammonia Toxicity Criteria

Scenario 3 extended scenarios 1 and 2 by comparing 

those results to the relevant Oregon dissolved oxygen, 

pH, and ammonia toxicity criteria. Chlorophyll a results 

from the model were not compared to the State of Oregon 

action level in this study because the TMDL was not 

written to demonstrate compliance with the chlorophyll a

criterion; rather, it was assumed that achieving compliance 

with the dissolved-oxygen and pH criteria would be more 

directly protective of aquatic life (Oregon Department 

of Environmental Quality, 2010). Water temperature was 

not included in this analysis because water temperature 

allocations to point and nonpoint sources were determined 

based on basin-specific rule language instead of instream 

analysis (oral commun., Daniel Turner, Oregon Department of 

Environmental Quality).

Water Quality Criteria

The relevant numeric dissolved oxygen, pH, and 

ammonia toxicity criteria for the Link-Keno reach were based 

on State of Oregon standards specific to the Link-Keno reach 

of the Klamath River (Oregon Department of Environmental 

Quality, 2011). During the modeling and analysis process 

to determine TMDL allocations, ODEQ examined water 

quality criteria compliance at seven locations in the LinkKeno reach: at the inflow locations of the Klamath Falls 

wastewater treatment plant (USGS model segment 4), South 

Suburban wastewater treatment plant (segment 8), Lost River 

Diversion Channel (segment 19), and Klamath Straits Drain 

(segment 69), as well as at monitoring sites Miller Island 

(segment 38), KRS12a (segment 78), and Keno (segment 95) 

(figs. 1 and 3). Prior analysis demonstrated that these selected 

locations were representative of dissolved oxygen conditions 

in the reach (Sullivan and others, 2012).

Dissolved Oxygen

The dissolved-oxygen standard for the Link-Keno reach 

of the Klamath River defines the numeric criteria as “...the 

dissolved oxygen may not fall below 6.5 mg/L as a 30-day 

mean minimum, 5.0 mg/L as a 7-day minimum mean, and 

may not fall below 4.0 mg/L as an absolute minimum...” 

when sufficient data are available to compute these statistics, 

as is the case with continuous monitor data or model results 

(Oregon Department of Environmental Quality, 2011). All 

three of these numeric criteria must be attained to achieve 

compliance. The “30-day mean minimum” is defined as the 

minimum of the 30 consecutive-day floating average of the 

tac13-0843_fig 04

0

2

4

6

8

10

12

105 90 75 60 45 30 15 0

Model segment

Keno Dam

Link River

Dissolved oxygen, in milligrams per liter

EXPLANATION

Flow direction

Scenario

 Base case (2007)

 1b

 2a

 2b

Figure 4. Simulated dissolved-oxygen 

concentration under the base case and for 

scenarios 1b, 2a, 2b in the Link-Keno reach, 

Klamath River, Oregon, on August 1, 2007. 

Scenario 1b represents Link-Keno reach point 

and nonpoint sources meeting Klamath River 

Total Maximum Daily Load (TMDL) allocations. 

Scenario 2a represents results considering 

the Upper Klamath Lake TMDL target was met. 

Scenario 2b is a combination of scenarios 1b and 

2a. Values are daily average, segment volumeaverage concentrations.
Model Scenarios 11

calculated daily mean, and the daily mean is computed such 

that “concentrations in excess of 100 percent of saturation are 

valued at the saturation concentration.” The “7-day minimum 

mean” is defined as the minimum of the 7 consecutive-day 

floating average of the daily minimum concentration. The 

“4.0 mg/L as an absolute minimum” is an instantaneous 

criterion and was checked with hourly results. The State 

of Oregon standards do not specify whether the numeric 

criteria were based on depth-averaged or volume-averaged 

concentrations. ODEQ used depth-averaged dissolvedoxygen concentrations to compare to these dissolved-oxygen 

criteria. A previous modeling study (Sullivan and others, 

2012) determined that dissolved oxygen depth-average 

concentrations in the upper Klamath River typically were 

lower than volume-average concentrations. Depth averaging 

gave relatively higher weight to small-volume areas near 

the channel bottom that often had lower dissolved-oxygen 

concentration. The current modeling study used volumeaverage dissolved-oxygen concentrations because that 

result was more representative of average dissolved-oxygen 

concentration when the entire cross section was considered.

Additional rule language for sources in this reach states 

that “no measurable reduction of dissolved oxygen” shall 

result, where “measurable reduction” is defined as “...no 

more than 0.20 mg/L for all anthropogenic activity.” This 

0.20 mg/L rule was one of the primary measures used during 

the determination of allocations for point and nonpoint sources 

for the Klamath River TMDL (oral commun., Daniel Turner, 

Oregon Department of Environmental Quality).

pH

The relevant Oregon pH standard for this reach of the 

Klamath River defines the numeric criteria as “...pH values 

may not fall outside the range of 6.5-9” (Oregon Department 

of Environmental Quality, 2011). ODEQ compared model 

results to the criteria at a depth of 1.1 m from the surface on 

an hourly basis at the seven compliance locations. The same 

approach was used in this study.

Ammonia Toxicity

Ammonia occurs in natural waters as either ammonium 

(NH4

+) or un-ionized ammonia (NH3). Un-ionized ammonia is 

the predominant form when the pH is greater than about 9.3, 

and is the form that is toxic to fish. The un-ionized form of 

ammonia increases as pH and temperatures increase. The State 

of Oregon ammonia toxicity criteria, based on that of the U.S. 

Environmental Protection Agency (EPA), are set according 

to concentrations of the un-ionized ammonia form and are a 

function of water temperature (T) and pH (U.S. Environmental 

Protection Agency, 1986). The numeric criteria equations take 

different forms depending on whether salmonids and other 

coldwater species are present; the upper Klamath River TMDL 

used equations that assumed that coldwater species were 

present (Oregon Department of Environmental Quality, 2010). 

The acute ammonia toxicity criteria were designed to protect 

fish against acute toxic effects such as loss of equilibrium, 

hyperexcitability, increased breathing, cardiac output, 

convulsions, coma, or death (U.S. Environmental Protection 

Agency, 1986). The chronic ammonia toxicity criteria were 

designed to protect fish from lower level concentration 

effects such as reduction in hatching success or growth, and 

pathological changes in gill, liver, and kidney tissues (U.S. 

Environmental Protection Agency, 1986). 

 The acute criteria, in milligrams per liter as NH3, are 

calculated as 0.52/FT/FPH/2, and the chronic criteria are 

calculated as 0.80/FT/FPH/Ratio. The equation parameters are 

defined as:

FT = 100.03(20-TCAP) ; TCAP ≤ T≤30

FT = 100.03(20-T) ; 0≤T≤TCAP

FPH = 1; 8≤pH≤9

FPH = (1 + 10(7.4-pH))/1.25; 6.5≤pH≤8

Ratio = 16; 7.7≤pH≤9

Ratio = (24 * 10(7.7-pH))/(1 + 10(7.4-pH)) ; 6.5≤pH≤7.7

TCAP = 20°C for acute criteria and 15°C for chronic

criteria, when salmonids or other sensitive cold water

species are present.

The acute criteria were applied using 1-hour average 

concentration of un-ionized ammonia. The chronic criteria 

were applied based on the 4-day average un-ionized 

ammonia concentrations. The EPA states that the equations 

should not be applied outside the pH range of 6.5 to 9.0 or a 

water temperature range of 0 to 30°C (U.S. Environmental 

Protection Agency, 1986). Because alternate equations were 

not provided for conditions outside this pH range, and because 

ODEQ applied these equations to all upper Klamath River 

conditions without modification, this study mirrored that 

approach. ODEQ applied the criteria during model analysis 

at a depth of 1.1 m from the surface at the seven compliance 

locations. The same method was followed for this study. 

The EPA criteria in the equations above are for un-ionized 

ammonia in units of milligrams per liter as NH3. In this report, 

the criteria for un-ionized ammonia in milligrams per liter as 

NH3 were converted to an equivalent concentration of total 

ammonia (ammonium plus ammonia) in milligrams per liter as 

nitrogen (N) using well-known equations for the speciation of 

ammonia as a function of pH and temperature. 
12 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Natural Conditions Effect on Criteria

In Oregon, all previously described numeric waterquality criteria can be superseded if it is determined that water 

quality under “natural conditions” would be of lower quality 

for a specific time and place. Oregon Administrative Rules 

state, “Where a less stringent natural condition... exceeds 

the numeric criteria... the natural condition supersedes the 

numeric criteria” (Oregon Department of Environmental 

Quality, 2011). For instance, if the numeric instantaneous 

dissolved-oxygen criterion is 4.0 mg/L, but analysis indicated 

that the dissolved-oxygen concentration under natural 

conditions for a certain place and time would be 3.8 mg/L, 

then 3.8 mg/L becomes the applicable criteria.

Natural conditions is defined as “conditions or 

circumstances affecting the physical, chemical, or biological 

integrity of a water of the state that are not influenced by past 

or present anthropogenic activities” (Oregon Department of 

Environmental Quality, 2011). Anthropogenic activity that 

modified flow began prior to 1900 in the Klamath Basin, 

when little to no quantitative flow or water-quality data were 

available. In the dissolved-oxygen criteria analyses for this 

report, model simulations to approximate natural conditions 

of water quality were constructed by assuming a level of 

improved water quality from Upper Klamath Lake and limited 

effects from nonpoint and point sources. These simulations 

are termed “reference condition” to acknowledge that they 

represent only an approximation of natural conditions. More 

specifics of the reference conditions model construction, and 

how the USGS-Watercourse-Reclamation reference conditions 

analysis differs from that used in the TMDL, are described in 

Sullivan and others (2012).

Results

Comparison to Dissolved-Oxygen Criteria

Measured and simulated dissolved-oxygen concentrations 

were well above the relevant criteria in winter, spring, and late 

fall. In the base case (scenario 3(1a)) conditions of 2006–09, 

dissolved-oxygen concentrations were less than the criteria in 

the Link-Keno reach of the Klamath River in summer through 

early fall (fig. 5). At that time of year, the river had large loads 

of decomposable organic matter, which consumed oxygen 

during decay. Water temperatures were warmer during this 

period, which decreased the solubility of oxygen in water. 

The maximum number of days that any of the three numeric 

criteria were not met in any scenario year ranged as high as 

143 days and tended to be at least about 100 days at most 

locations in the base case (table 3); in the years modeled, the 

30-day criteria were more difficult to attain compared to the 

7-day or instantaneous criteria, so the results in table 3 are for 

the 30-day criteria analysis. The average concentration below 

the criteria for that period ranged from 1.2 to 3.7 mg/L for key 

locations in the base case (table 3).

Under base case conditions, some part of the Link-Keno 

reach was less than dissolved oxygen criteria for at least 

3 months in summer in all years modeled. Dissolved oxygen 

conditions generally worsened from upstream to downstream 

for several reasons: inflowing oxygen concentrations were 

elevated from aeration at Link Dam and Link River, oxygen 

demand increased downstream as algae and particulate organic 

matter settled and decayed, and inflows of oxygen-demanding 

material or low dissolved-oxygen levels entered the river from 

point sources (for example, Klamath Falls and South Suburban 

wastewater treatment plants) and nonpoint sources (Lost River 

Diversion Channel and Klamath Straits Drain) along the reach.

Setting Link River nutrient and organic matter 

concentrations at lower values (scenario 3(2a)) to reflect the 

Upper Klamath Lake TMDL target led to increased attainment 

of dissolved-oxygen criteria in the upper Klamath River. 

In that scenario, the upper areas of the reach, close to Link 

River, improved from levels less than the dissolved-oxygen 

criteria for 3 months of the year (scenario 3(1a)) to attaining 

the criteria at all locations and times (scenario 3(2a); table 3). 

The more downstream reach of this study area, closer to 

Keno Dam, was still less than the dissolved-oxygen criteria 

in this scenario, although the period was shorter, and when 

digressions occurred, concentrations were much closer to the 

criteria. For example, in the 2009 base case 3(1a), at segment 

69 at the Klamath Straits Drain inflow, for the 142 days when 

dissolved-oxygen criteria were not attained, waters were 

less than the criteria by an average of 3.4 mg/L. In scenario 

3(2a), that location did not attain dissolved-oxygen criteria on 

86 days, but the concentrations were less than the criteria by 

an average of 0.1 mg/L for the 86 days.

Simulating point and nonpoint sources along the 

Link-Keno reach in compliance with Klamath River 

TMDL allocations (scenario 3(1b)) shifted the river toward 

compliance with dissolved-oxygen criteria, but in fewer 

locations and to a lesser amount than simulating Link River 

inflows in compliance with the Upper Klamath Lake TMDL. 

Simulating in-reach point and nonpoint sources to meet 

TMDL allocations was most effective at bringing the river 

into compliance with water quality criteria when Link River 

was already at the Upper Klamath Lake TMDL target. For 

Keno (segment 95) in 2008, the base case results were less 

than the criteria for 142 days by an average of 3.2 mg/L; when 

Link River TMDL compliance was assumed, water quality 

improved and the dissolved-oxygen concentrations were 

less than the criteria on 82 days by an average of 0.3 mg/L 

(table 3). Adding in Klamath River point and nonpoint 

source TMDL compliance provided sufficient additional 

improvement to achieve dissolved oxygen compliance at Keno 

for the entire year.
Model Scenarios 13

Table 3. Number of days dissolved oxygen was simulated to be less than the 30-day criteria (and the average amount less than the 

criteria) at selected Oregon Department of Environmental Quality compliance locations for scenario 3 under the base case and Total 

Maximum Daily Load scenarios, Klamath River, Oregon, for years 2006–09.

[30-day criteria is based on Oregon Department of Environmental Quality regulations (Oregon Department of Environmental Quality, 2011). Abbreviations:

segment, model segment; TMDL, total maximum daily load; WWTP, wastewater treatment plant; mg/L, milligram per liter]

Scenario

Days less than 30-day dissolved oxygen criteria (and average less than the criteria, in mg/L)

Klamath River at 

WWTP inflows 

(segments 4, 8)

Klamath River at 

Lost River Diversion 

Channel inflow

Klamath River at 

Miller Island

Klamath River at 

Klamath Straits 

Drain inflow

Klamath River 

at Keno

Segment 8 Segment 19 Segment 38 Segment 69 Segment 95

2006

3(1a) Base case (current conditions) 101 (1.2) 119 (1.8) 124 (2.7) 127 (2.8) 128 (2.7)

3(1b) Sources at TMDL allocations 101 (1.2) 118 (1.7) 124 (2.6) 125 (2.6) 124 (2.4)

3(2a) Link River at TMDL target 0 0 16 (0.1) 85 (0.3) 27 (0.5)

3(2b) Link River and sources at TMDL 0 0 0 69 (0.2) 0

2007

3(1a) Base case (current conditions) 98 (1.8) 111 (2.5) 123 (3.1) 122 (3.1) 108 (2.3)

3(1b) Sources at TMDL allocations 98 (1.8) 110 (2.5) 121 (3.1) 114 (3.2) 102 (2.1)

3(2a) Link River at TMDL target 0 0 9 (0.1) 69 (0.4) 0

3(2b) Link River and sources at TMDL 0 0 0 62 (0.3) 0

2008

3(1a) Base case (current conditions) 97 (2.3) 119 (3.1) 138 (3.3) 143 (3.1) 142 (3.2)

3(1b) Sources at TMDL allocations 97 (2.3) 119 (3.1) 137 (3.3) 141 (3.0) 140 (3.0)

3(2a) Link River at TMDL target 0 4 (0.2) 22 (0.2) 41 (0.1) 82 (0.3)

3(2b) Link River and sources at TMDL 0 3 (0.2) 20 (0.2) 19 (0.1) 0

2009

3(1a) Base case (current conditions) 104 (2.3) 122 (3.3) 136 (3.7) 142 (3.4) 140 (3.5)

3(1b) Sources at TMDL allocations 103 (2.3) 122 (3.3) 136 (3.6) 140 (3.4) 136 (3.4)

3(2a) Link River at TMDL target 0 0 0 86 (0.1) 78 (0.3)

3(2b) Link River and sources at TMDL 0 0 0 57 (0.1) 0
14 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

tac13-0843_fig 05

0.0

2.0

4.0

6.0

8.0

10.0

12.0

14.0

Dissolved oxygen, milligrams per liter

Hourly

0.0

2.0

4.0

6.0

8.0

10.0

12.0

14.0

Dissolved oxygen, milligrams per liter

7-day

0.0

2.0

4.0

6.0

8.0

10.0

12.0

14.0

Dissolved oxygen, milligrams per liter

2007

30-day

Jan. Feb. Mar. Apr. May June July Aug. Sept. Oct. Nov. Dec.

EXPLANATION

4.0 milligram per liter (mg/L) criteria

Final criteria

Hourly (scenario)

Hourly (reference)

EXPLANATION

5.0 mg/L criteria

Final criteria

7-day minimum mean (scenario)

7-day minimum mean (reference)

EXPLANATION

6.5 mg/L criteria

Final criteria

30-day mean (scenario)

30-day mean (reference)

Figure 5. Dissolved-oxygen concentrations for the base case scenario (3[1a]) and reference conditions (3[nc]) scenarios, 

and hourly, 7-, and 30-day dissolved-oxygen criteria for the upper Klamath River at Miller Island (model segment 38), Oregon, 

2007. Scenario descriptions are shown in table 2.
Model Scenarios 15

Comparison to pH Criteria

The pH in the Link-Keno reach was greater than the 

9.0 maximum criterion during some periods in summer under 

base case conditions when algal blooms occurred (figs. 6A, 

6B). The minimum pH criterion of 6.5 was attained in all 

model runs for scenarios 1 to 3. Unlike dissolved oxygen, 

where digressions from the criteria were more common in 

the mid and downstream reaches, pH 9.0 criteria exceedances 

were most frequent in the upstream reaches (table 4). A 

primary cause of elevated pH was related to algal blooms in 

Upper Klamath Lake, which enter the upper Klamath River 

through the Link River. Algal populations decreased from 

upstream to downstream in the Link-Keno reach (Sullivan 

and others 2008, 2009), so pH values also decreased in the 

downstream direction.

Table 4. Number of days pH was simulated to be greater than the 9.0 criteria (and the average amount greater than the criteria) at 

selected Oregon Department of Environmental Quality compliance locations for scenario 3 under the base case and Total Maximum 

Daily Load scenarios, Klamath River, Oregon, for years 2006–09.

[2007 runs were bracketed by also using input total inorganic carbon calculated with pH during low-bloom conditions (leftmost values when a range is given) 

for the Link River, Lost River Diversion Channel, and Klamath Straits Drain inputs. Abbreviations: TMDL, total maximum daily load; segment, model 

segment; WWTP, wastewater treatment plant]

Scenario

Days out of compliance with pH criteria (and average amount greater than the criteria)

Klamath River at 

WWTP inflows 

(segments 4, 8)

Klamath River at 

Lost River Diversion 

Channel inflow

Klamath River at 

Miller Island

Klamath River at 

Klamath Straits 

Drain inflow

Klamath River 

at Keno

Segment 8 Segment 19 Segment 38 Segment 69 Segment 95

2006

3(1a) Base case (current conditions) 90 (0.30) 69 (0.21) 53 (0.19) 28 (0.13) 8 (0.10)

3(1b) Sources at TMDL allocations 90 (0.30) 74 (0.22) 55 (0.20) 29 (0.14) 14 (0.11)

3(2a) Link River at TMDL target 112 (0.51) 93 (0.40) 94 (0.37) 73 (0.28) 62 (0.23)

3(2b) Link River and sources at TMDL 112 (0.51) 101 (0.41) 104 (0.38) 86 (0.30) 79 (0.30)

2007

3(1a) Base case (current conditions) 52 (0.44) 32 (0.55) 24 (0.72) 21 (0.58) 24 (0.55)

3(1b) Sources at TMDL allocations 53 (0.43) 33 (0.55) 24 (0.72) 22–23 

(0.58–0.57)

26–27 

(0.52–0.55)

3(2a) Link River at TMDL target 7–105

(0.08-0.46)

9–77

(0.08–0.54)

23–78

(0.15–0.51)

18–64

(0.24–0.47)

52–93

(0.23–0.50)

3(2b) Link River and sources at TMDL 6–106

(0.07–0.46)

8–78

(0.06–0.54)

23–79

(0.13–0.50)

19–71

(0.22–0.46)

78–102

(0.23–0.57)

2008

3(1a) Base case (current conditions) 102 (0.44) 69 (0.39) 49 (0.36) 24 (0.18) 9 (0.11)

3(1b) Sources at TMDL allocations 103 (0.44) 71 (0.39) 49 (0.36) 29 (0.18) 15 (0.12)

3(2a) Link River at TMDL target 142 (0.65) 127 (0.54) 110 (0.51) 73 (0.43) 61 (0.38)

3(2b) Link River and sources at TMDL 143 (0.65) 135 (0.53) 119 (0.51) 92 (0.38) 79 (0.39)

2009

3(1a) Base case (current conditions) 90 (0.45) 68 (0.35) 43 (0.27) 13 (0.27) 13 (0.23)

3(1b) Sources at TMDL allocations 91 (0.44) 70 (0.35) 45 (0.27) 15 (0.31) 15 (0.29)

3(2a) Link River at TMDL target 106 (0.74) 101 (0.69) 98 (0.63) 83 (0.45) 82 (0.40)

3(2b) Link River and sources at TMDL 106 (0.74) 101 (0.70) 99 (0.64) 88 (0.48) 90 (0.48)
16 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

tac13-0843_fig 06a

2007

Jan. Feb. Mar. Apr. May June July Aug. Sept. Oct. Nov. Dec.

6.0

7.0

8.0

9.0

10.0

11.0

pH

pH

EXPLANATION

Minimum criteria

Maximum criteria

Hourly (scenario)

10.0

15.0

20.0

Ammonia, in milligrams per liter as N

Ammonia (Acute)

EXPLANATION

Hourly acute criteria

Hourly (scenario)

0

0.5

0

0.5

1.0

1.5

2.0

2.5

Ammonia, in milligrams per liter as N

Ammonia (Chronic)

EXPLANATION

4-day average chronic criteria

4-day average (scenario)

A

Figure 6. pH and ammonia concentrations from scenario [3(2a)], and criteria for pH and acute and chronic ammonia toxicity 

for the upper Klamath River at Miller Island (model segment 38), Oregon, 2007. For comparison, Link River total inorganic 

carbon was calculated based on (A) current conditions pH and (B) estimated low-bloom pH. Scenario descriptions are shown 

in table 4.
Model Scenarios 17

tac13-0843_fig 06b

Jan. Feb. Mar. Apr. May June July Aug. Sept. Oct. Nov. Dec.

2007

6.0

7.0

8.0

9.0

10.0

11.0

pH

pH

10.0

15.0

20.0

Ammonia, in milligrams per liter as N

Ammonia (Acute)

0

0.5

0

0.5

1.0

1.5

2.0

2.5

Ammonia, in milligrams per liter as N

Ammonia (Chronic)

EXPLANATION

Minimum criteria

Maximum criteria

Hourly (scenario)

EXPLANATION

Hourly acute criteria

Hourly (scenario)

EXPLANATION

4-day average chronic criteria

4-day average (scenario)

B

Figure 6.—Continued
18 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

The pH effects associated with compliance of Upper 

Klamath Lake/Link River and in-reach tributary sources 

with TMDL targets and allocations were more difficult to 

predict. The pH was not only related to in-reach reactions 

that are capably modeled by the CE-QUAL-W2 model, but 

also the TIC and alkalinity of the inflows, which likely would 

change if the upstream watersheds were managed or altered 

to meet upstream TMDL allocations. Thus, the effect on 

TIC and alkalinity could be different depending on upstream 

management actions. For year 2007, scenarios 3(1b), 3(2a), 

and 3(2b) were run twice, first by assuming that inflow pH 

and TIC would be unchanged after the Klamath River TMDL 

allocations or Upper Klamath Lake target were met, and again 

by estimating the pH and TIC conditions that might occur 

in the presence of smaller algal blooms in those inflows. 

The difference in model output was minor in 3(1b), but 

significant in 3(2a) and 3(2b), the runs that simulated Link 

River with Upper Klamath Lake at its TMDL target. As an 

example, at Miller Island (segment 38) in 2007 for scenario 

3(2a), the model predicted that the pH would exceed the 

criteria for 78 days if inflow pH and TIC were unchanged 

or above the criteria for only 23 days if inflow pH and TIC 

were estimated to account for smaller algal blooms upstream 

(table 4, figs. 6A, 6B).

With the model predicting elevated pH conditions 

to occur when TMDLs were met, such as in scenario 

3(2b) compared to the base case, the cause of the elevated 

conditions provides a good illustration of the difficulties in 

accurately predicting a future pH condition. Under base-case 

conditions, pH tends to increase or decrease largely depending 

on the levels of photosynthesis and respiration that occur. 

Photosynthesis removes dissolved carbon dioxide (essentially 

carbonic acid) from the water, and respiration processes 

release carbon dioxide (carbonic acid) back into the water. 

Removing acid increases the pH, and adding acid decreases 

the pH. During a bloom, the pH tends to be high because 

of the removal of carbon dioxide for the production of 

biomass, whereas after a bloom declines, the pH decreases to 

a level that tends to be less than the maximum pH criterion. 

During a large algal bloom in Upper Klamath Lake, the pH 

is high and TIC concentration is low in Link River. In the 

Link-Keno reach, substantial amounts of TIC are released 

from decomposing algae and organic material, allowing the 

pH to decrease downstream. If a model scenario removed 

large populations of algae from the Link River inflow but 

did not adjust the pH or TIC, then the pH in the Link-Keno 

reach tended to stay elevated because the amount of carbon 

entering the reach was too small to replenish the TIC through 

subsequent decomposition and respiration processes. In 

estimating the effects of management activities that might 

decrease upstream inputs of algal populations, downstream pH 

conditions depend greatly on the pH and TIC of the inflows, 

which is the reason the analysis in this report bracketed a 

range of potential conditions for one of the modeled years.

A natural conditions analysis was not undertaken for 

the pH criteria in this study. If natural conditions were taken 

into account, for some periods when the pH was simulated to 

exceed the pH 9.0 criterion, natural conditions pH also may 

also have been elevated, causing the relevant pH criteria to be 

greater than 9.0. Therefore, the number of days the criterion 

was exceeded may be overstated in this analysis; however, this 

was considered a conservative assumption.

Comparison to Ammonia Toxicity Criteria

Numeric ammonia toxicity criteria vary in space and 

time because the criteria are based on pH and temperature. In 

winter when pH values were near-neutral and temperatures 

were low, the criteria were relatively high. Although ammonia 

concentrations were elevated during winter, the acute and 

chronic ammonia toxicity criteria were even greater at that 

time of year (figs. 6A, 6B). During summer, however, when 

pH was elevated and temperatures were warm, the calculated 

ammonia toxicity criteria decreased, so it was more likely that 

the ammonia criteria would be exceeded. 

Upper Klamath River waters were simulated to exceed 

the acute ammonia toxicity criteria between 0 and 27 days for 

the base case conditions for the years and selected locations 

shown in table 5. Exceedances of the chronic ammonia 

toxicity criteria were simulated to be more frequent, between 

27 and 118 days for the base case (table 6), and most common 

in the upstream part of the reach nearer Link River. Similar 

to the pH criteria analysis, the simulation of exceedances of 

the chronic ammonia toxicity criteria was sensitive to inflow 

TIC values. For example, at Miller Island (segment 38) for 

scenario 3(2a) in 2007, the number of days exceeding the 

criteria varied from 83 to 29 depending on whether the TIC 

was calculated from base case pH conditions or a potentially 

lower pH under conditions with less algae (table 6, fig. 6A, 

6B). The simulated range of exceedance days, however, 

illustrates the importance of determining the effect of 

upstream management activities on pH conditions; for these 

simulations, insufficient information was available for these 

scenarios to provide estimates that are more certain. 

A natural conditions analysis was not undertaken in this 

study to assess the potential ammonia toxicity conditions in 

that reference condition.
Model Scenarios 19

Table 5. Number of days acute ammonia toxicity was greater than the criteria (and average amount greater than the criteria) at 

selected Oregon Department of Environmental Quality compliance locations for scenario 3 under the base case and Total Maximum 

Daily Load scenarios, Klamath River, Oregon, for years 2006–09.

[2007 runs were bracketed by also using total inorganic carbon calculated with pH during low-bloom conditions (leftmost values when a range is given) for the 

Link River, Lost River Diversion Channel, and Klamath Straits Drain inputs. Abbreviations: TMDL, total maximum daily load; segment, model segment; N, 

nitrogen; WWTP, wastewater treatment plant; mg/L, milligram per liter]

Scenario

Days greater than acute ammonia toxicity criteria 

(and average greater than the criteria, as ammonia, in mg/L N)

Klamath River at 

WWTP inflows 

(segments 4, 8)

Klamath River at 

Lost River Diversion 

Channel inflow

Klamath River at 

Miller Island

Klamath River at 

Klamath Straits 

Drain inflow

Klamath River 

at Keno

Segment 8 Segment 19 Segment 38 Segment 69 Segment 95

2006

3(1a) Base case (current conditions) 0 2 (0.03) 14 (0.06) 8 (0.08) 1 (0.05)

3(1b) Sources at TMDL allocations 1 (0.01) 2 (0.03) 14 (0.06) 8 (0.07) 2 (0.04)

3(2a) Link River at TMDL target 1 (0.01) 0 0 0 0

3(2b) Link River and sources at TMDL 0 0 0 0 0

2007

3(1a) Base case (current conditions) 6 (0.04) 13 (0.13) 18 (0.24) 18 (0.31) 19 (0.32)

3(1b) Sources at TMDL allocations 6 (0.04) 13 (0.13) 18 (0.24) 18 (0.31) 19 (0.32)

3(2a) Link River at TMDL target 0 0 0–7

(0.00–0.02)

0–11

(0.00–0.08)

0–5

(0.00–0.03)

3(2b) Link River and sources at TMDL 0 0 0–7

(0.00–0.02)

0–10

(0.00–0.08)

0–2 

(0.00–0.03)

2008

3(1a) Base case (current conditions) 4 (0.02) 20 (0.07) 27 (0.14) 16 (0.13) 1 (0.08)

3(1b) Sources at TMDL allocations 4 (0.02) 20 (0.07) 26 (0.14) 16 (0.13) 1 (0.08)

3(2a) Link River at TMDL target 0 0 5 (0.01) 17 (0.04) 4 (0.01)

3(2b) Link River and sources at TMDL 0 0 4 (0.01) 12 (0.03) 0

2009

3(1a) Base case (current conditions) 0 6 (0.01) 4 (0.02) 1 (0.02) 0

3(1b) Sources at TMDL allocations 0 6 (0.01) 4 (0.02) 1 (0.02) 0

3(2a) Link River at TMDL target 0 0 0 8 (0.01) 0

3(2b) Link River and sources at TMDL 0 0 0 6 (0.01) 0
20 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Table 6. Number of days chronic ammonia toxicity was greater than criteria (and average amount greater than the criteria) at selected 

Oregon Department of Environmental Quality compliance locations for scenario 3 under the base case and Total Maximum Daily Load 

scenarios, Klamath River, Oregon, for years 2006–09.

[2007 runs were bracketed by also using TIC calculated with pH during low-bloom conditions (leftmost values when a range is given) for the Link River, Lost 

River Diversion Channel, and Klamath Straits Drain inputs. Abbreviations: TMDL, total maximum daily load; segment, model segment; N, nitrogen; WWTP, 

wastewater treatment plant; mg/L, milligram per liter]

Scenario

Days greater than chronic ammonia toxicity criteria 

(and average greater than the criteria, as ammonia, in mg/L N)

Klamath River at 

WWTP inflows 

(segments 4, 8)

Klamath River at 

Lost River Diversion 

Channel inflow

Klamath River at 

Miller Island

Klamath River at 

Klamath Straits 

Drain inflow

Klamath River 

at Keno

Segment 8 Segment 19 Segment 38 Segment 69 Segment 95

2006

3(1a) Base case (current conditions) 111 (0.19) 101 (0.21) 98 (0.29) 79 (0.29) 68 (0.28)

3(1b) Sources at TMDL allocations 111 (0.19) 102 (0.20) 97 (0.28) 78 (0.28) 70 (0.27)

3(2a) Link River at TMDL target 122 (0.12) 117 (0.10) 119 (0.14) 109 (0.16) 101 (0.15)

3(2b) Link River and sources at TMDL 123 (0.12) 119 (0.10) 118 (0.13) 110 (0.14) 114 (0.11)

2007

3(1a) Base case (current conditions) 84 (0.21) 74 (0.32) 69 (0.35) 54 (0.33) 60 (0.34)

3(1b) Sources at TMDL allocations 85 (0.21) 74 (0.32) 70 (0.35) 50–53 

(0.33–0.32)

62–62

(0.33–0.32)

3(2a) Link River at TMDL target 11–110 

(0.02–0.07)

20–76

(0.05–0.12)

29–83

(0.09–0.16)

33–86

(0.08–0.20)

83–91

(0.09–0.12)

3(2b) Link River and sources at TMDL 12–111

(0.02–0.07)

19–81

(0.05–0.12)

38–85 

(0.08–0.16)

28–87 

(0.08–0.18)

65–86 

(0.07–0.08)

2008

3(1a) Base case (current conditions) 118 (0.16) 82 (0.23) 71 (0.35) 49 (0.37) 47 (0.34)

3(1b) Sources at TMDL allocations 118 (0.16) 87 (0.23) 73 (0.34) 49 (0.35) 46 (0.34)

3(2a) Link River at TMDL target 137 (0.08) 134 (0.09) 149 (0.12) 134 (0.15) 109 (0.17)

3(2b) Link River and sources at TMDL 136 (0.08) 144 (0.09) 158 (0.12) 151 (0.13) 133 (0.12)

2009

3(1a) Base case (current conditions) 118 (0.19) 110 (0.22) 94 (0.26) 43 (0.21) 27 (0.20)

3(1b) Sources at TMDL allocations 119 (0.19) 112 (0.22) 95 (0.26) 44 (0.20) 28 (0.18)

3(2a) Link River at TMDL target 129 (0.13) 124 (0.14) 119 (0.16) 98 (0.20) 95 (0.18)

3(2b) Link River and sources at TMDL 129 (0.13) 125 (0.15) 121 (0.16) 98 (0.18) 96 (0.15)
Model Scenarios 21

Scenario 4. Compare USGS Model and TMDL 

Model Results

As part of the TMDL process, ODEQ and Tetra Tech, 

Inc. developed a water-quality model for almost the entire 

Klamath River, including the Link-Keno reach, based 

on a CE-QUAL-W2 model previously developed for a 

dam-relicensing process by Watercourse (Watercourse 

Engineering, Inc., 2004). That model from Watercourse was 

used to construct a modified model for the Link-Keno reach 

for the years 2000 and 2002 (Tetra Tech, Inc., 2009). The 

data used to drive the model, however, did not include direct 

measurements of organic matter concentrations, organic 

matter partitioning, or algae species. The technical basis of 

the TMDL model for the Link-Keno reach was reviewed and 

evaluated previously by the USGS (Rounds and Sullivan, 

2009 and 2013).

Methods

The TMDL model and the more recent USGS model 

were developed for different years, so their specific predictions 

cannot be compared directly. A qualitative comparison was 

made by Sullivan and others (2012) with the 2006–09 USGS 

input files applied to the TMDL model. That comparison 

provided a qualitative way to examine the effect of differences 

between the models in organic matter partitioning, algae 

algorithms, parameter values, bathymetry, and the nature 

of the sediment oxygen demand formulation. In the current 

analysis, the comparison was rerun using the updated USGS 

model that includes macrophytes and enhanced pH buffering 

(Sullivan and others, 2013). 

Results

Comparisons of model results for most constituents were 

similar to those documented by Sullivan and others (2012); 

therefore, only pH, the newest calibrated constituent of the 

USGS model, is discussed here. Use of the updated USGS 

model with enhanced pH buffering produced results that more 

closely compare to the measured pH (fig. 7). Most versions 

of CE-QUAL-W2, including that used for the TMDL model, 

only consider carbonate alkalinity in the calculation of pH, and 

do not consider buffering by organic matter, orthophosphorus, 

or ammonia. Buffering by organic matter was demonstrated 

to be important in the upper Klamath River ecosystem by 

Sullivan and others (2013). The addition of macrophytes to 

the USGS model also helped to improve the simulation of pH 

in the Link-Keno reach, because photosynthetic activity tends 

to increase the pH of the river. The influence of macrophytes 

on pH was especially important in the downstream part 

of the model domain near Keno, where macrophytes were 

most populous.

Jan. Apr. July Oct. Jan. Apr. July Oct. Jan. Apr. July Oct. Jan. Apr. July Oct.

2007

6.5

10.5

6.5

10.5

pH

Keno

Top

Bottom

KRS12a Miller Island Railroad Bridge

EXPLANATION

Measured

USGS model

TMDL model, scenario 4

Figure 7. Comparison of measured daily average pH with daily average model results from the calibrated USGS model and 

scenario 4 TMDL model (2007 inputs applied to TMDL model setup) for sites in the Link-Keno reach of the Klamath River, 

Oregon, 2007.
22 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Scenario 5. Particulate Matter Shunting

For scenario 5, the effect of shunting or diverting 

particulate material away from withdrawal canals was 

examined; particulate material suspended in the water column 

remained in the Klamath River when water was withdrawn 

through canals to the Lost River basin. Although the work 

presented here primarily focuses on the effects in the Klamath 

River between Link River and Keno Dam, a potential future 

extension of this scenario could examine how this decrease 

in particulate material into the Lost River might affect water 

quality in that basin.

Methods

In the current study, the scenario 5 setup was unchanged 

from Sullivan and others (2012), except that this scenario was 

run with the updated model that includes macrophytes and 

enhanced pH buffering (Sullivan and others, 2013).

In brief, although water withdrawals from the Klamath 

River continued for all or part of each year to the A Canal, 

Lost River Diversion Channel, North Canal, and Ady Canal, 

particulate material was assumed “filtered” so that it stayed in 

the Klamath River instead of leaving the river through these 

canals. The shunted particulate matter included inorganic 

suspended sediment, labile particulate organic matter, 

refractory particulate organic matter, and all algae types 

(blue-green algae, diatoms, and other algae). The A Canal 

is outside the Link-Keno model boundary, so the effect of 

shunting particulate matter was calculated and then that load 

was added to the Link River inflow. Shunting for the other 

canals was accomplished within the model by alterations to 

the CE-QUAL-W2 source code (Sullivan and others, 2012), 

wherein particulate matter simply remained in the river and 

was not withdrawn.

If less particulate matter were exported into the Lost 

River basin, it is possible that decreased loads of certain 

materials would return to the Klamath River through canals, 

which bring water from the Lost River basin to the Klamath 

River. Because the Lost River basin was outside the model 

boundary, potential variations in return flow water quality for 

the Lost River Diversion Channel and Klamath Straits Drain 

returns was examined with a bracketing approach. Scenario 5a 

represented an end member that assumed base case return 

flow concentrations. Scenario 5c represented an end member 

that assumed dissolved-oxygen concentrations were at 

saturation and that concentrations of particulate and dissolved 

nutrients, algae, and organic matter were zero for the Lost 

River Diversion Channel and Klamath Straits Drain returns. 

Clearly, zero concentrations of those constituents is unlikely 

in any future condition, but scenario 5c serves to examine 

the potential effect of large changes in the characteristics of 

the return flows. Scenario 5b instituted intermediate changes 

to return flow concentrations in the Lost River Diversion 

Channel and Klamath Straits Drain. 

Results

In general, scenario 5 results using the updated model 

indicated that shunting would degrade water quality in the 

Link-Keno reach compared to the base case. For instance, the 

model predicted a June–October decrease in Link-Keno reach 

volume-average dissolved-oxygen concentration of between 

1.3 and 2.3 mg/L, compared to the base case (1a), depending 

on year and scenario (table A4, fig. 8), and June–October 

reach-averaged concentrations of dissolved oxygen in the 

base case (1a) were already low (2.85-4.60 mg/L) (table A4). 

Ammonia, chlorophyll a, particulate organic carbon, total 

nitrogen, and accumulated sediment concentrations all 

increased in these shunting scenarios, consistent with the 

increased input loads of particulate material. The simulations 

predicted that nitrate concentrations would decrease, primarily 

because of lower dissolved-oxygen concentrations to support 

ammonia nitrification. Orthophosphorus, total phosphorus, and 

dissolved organic carbon concentrations either increased or 

decreased depending on the scenario (tables A3 and A4).

Variability in the characteristics of the return flow 

water in Lost River Diversion Channel and Klamath Straits 

Drain, as expressed in the differences in simulation results 

from scenarios 5a, 5b, and 5c, had only a minor effect on 

Link-Keno water quality (tables A3 and A4). As discussed in 

Sullivan and others (2012), several factors contributed to this 

result, including the fact that point and nonpoint sources had 

relatively small effects on upper Klamath River dissolvedoxygen concentrations when Link River particulate loads 

were high.

0

2

4

6

8

10

12

105 90 75 60 45 30 15 0

Model segment

Keno Dam

Link River

Dissolved oxygen, in milligrams per liter

EXPLANATION

Flow direction

Scenario

 Base case (2007)

 5a

 5b

 5c

Figure 8. Simulated dissolved-oxygen 

concentration under the base case and for 

scenario 5 in the Link-Keno reach of the Klamath 

River, Oregon, August 1, 2007. Scenario 5 simulated 

the effect of filtering canal withdrawals from the 

Klamath River, such that particulate matter was 

kept in the Klamath River. Values are daily average, 

segment volume-average concentrations.
Model Scenarios 23

Scenario 6. Decrease Particulate Organic 

Matter and Blue-Green Algae in Link River

The objective of scenario 6 was to decrease the amount 

of particulate organic material and algae in Link River and 

assess downstream spatial and temporal water quality impacts. 

Removal of algae and particulate material has been postulated 

as a potential management alternative for improving the water 

quality in the upper Klamath River (for example, Stillwater 

Sciences and others, 2012). Load decreases of 25, 50, and 

90 percent were simulated for 2006–09 assuming that load 

decreases applied for the entire calendar year, as well as for 

the June 15–October 31 time period (tables 7, 8).

Methods

The decrease in particulate organic matter and algae 

loads was envisioned as a treatment approach using physical 

removal of larger-size particulate material, with active 

removal that could be turned on when needed. The removal 

site was assumed to be located either at Link Dam or in Link 

River, as long as the treatment resulted in a decrease of Link 

River particulate matter and algae loads to the Klamath River. 

In recent years, summer blue-green algae populations in Link 

River have been dominated by the blue-green algae species 

Aphanizomenon flos aquae, which forms large filaments 

and flakes visible to the naked eye. The particulate organic 

matter during the time of summer blue-green algal blooms 

was assumed to be dead algae derived from the blooms. In 

these model scenarios, Link River inflow blue-green algae 

and particulate organic matter concentrations, both labile and 

refractory, were decreased by identical percentages to preserve 

the ratio between the algal standing crop and its contribution 

to particulate organic matter. If a trophic shift or other change 

resulted in a shift from the currently dominant Aphanizomenon 

flos aquae to a species that was less prone to produce 

particulate organic matter or perhaps more prone to produce 

smaller particles of organic matter, then this assumption could 

be revisited.

Table 7. Annual particulate organic material and algae load decreases for scenario 6, Link-Keno reach 

of the Klamath River, Oregon, 2006–09.

[Annual load decreases are the sum(s) of the monthly averaged volume (Q × time) multiplied by the monthly averaged 

concentration. Abbreviations: POM, particulate organic matter; ALG1, blue-green algae; C, carbon; N, nitrogen; P, 

phosphorus]

Year

25 percent load decrease (metric tons)

POM ALG1 POM+ALG1

Associated nutrient decrease

Organic C Organic N Organic P

2006 788 866 1,655 761 97.6 6.62

2007 679 833 1,512 695 89.2 6.05

2008 1,480 697 2,176 1,001 128 8.71

2009 1,808 470 2,278 1,048 134 9.11

Year

50 percent load decrease (metric tons)

POM ALG1 POM+ALG1

Associated nutrient decrease

Organic C Organic N Organic P

2006 2,561 1,732 4,293 1,975 253 17.2

2007 1,651 1,665 3,317 1,526 196 13.3

2008 2,438 1,394 3,831 1,762 226 15.3

2009 3,478 940 4,418 2,032 261 17.7

Year

90 percent load decrease (metric tons)

POM ALG1 POM+ALG1

Associated nutrient decrease

Organic C Organic N Organic P

2006 4,982 3,118 8,100 3,726 478 32.4

2007 3,184 2,998 6,182 2,844 365 24.7

2008 4,514 2,508 7,023 3,231 414 28.1

2009 6,479 1,693 8,171 3,759 482 32.7
24 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Table 8. Particulate organic material and algae load decreases (June 15–October 31) for scenario 6, 

Link-Keno reach of the Klamath River, Oregon, 2006–09.

[Load decreases are the sum(s) of the monthly averaged volume (Q × time) multiplied by the monthly averaged concentration. 

Abbreviations: POM, particulate organic matter; ALG1, blue-green algae; C, carbon; N, nitrogen; P, phosphorus]

Year

25 percent load decrease (metric tons)

POM ALG1 POM+ALG1

Associated nutrient decrease

Organic C Organic N Organic P

2006 416 782 1,198 551 70.7 4.79

2007 353 827 1,179 542 69.6 4.72

2008 1,079 691 1,770 814 104 7.08

2009 1,454 427 1,880 865 111 7.52

Year

50 percent load decrease (metric tons)

POM ALG1 POM+ALG1

Associated nutrient decrease

Organic C Organic N Organic P

2006 832 1,565 2,396 1,102 141 9.58

2007 705 1,653 2,359 1,085 139 9.43

2008 2,158 1,382 3,540 1,629 209 14.2

2009 2,907 853 3,760 1,730 222 15.0

Year

90 percent load decrease (metric tons)

POM ALG1 POM+ALG1

Associated nutrient decrease

Organic C Organic N Organic P

2006 1,497 2,816 4,313 1,984 254 17.3

2007 1,269 2,976 4,245 1,953 250 17.0

2008 3,884 2,488 6,373 2,931 376 25.5

2009 5,233 1,536 6,768 3,113 399 27.1

Concentrations of smaller-sized particulate materials 

remained unchanged in the model input files. For instance, 

concentrations of other algae groups were not adjusted in this 

scenario and concentrations of inorganic suspended sediment 

also were assumed to be unchanged. For most of the year, 

particularly during low flow periods, inorganic suspended 

sediment would be made up of relatively small sized clay 

particles, so approaches designed to catch larger algae and 

particulate organic matter were assumed not to target this 

material. Larger suspended inorganic particles from tributary 

sources may be present in winter during storms, but such 

conditions were usually of short duration.

For each year, concentrations of particulate organic 

matter and blue-green algae were decreased by 25, 50, and 

90 percent in the Link River model input file (tables 7, 8). 

Removal was simulated to occur during two times of the year: 

January 1 through December 31 (“year-round”), and June 15 

through October 31 (“seasonal”). The seasonal scenario was 

intended to simulate removal only for the summer and early 

autumn when loads of particulate organic matter and algae 

were greatest (fig. 2).

The load decreases of particulate organic matter and algae 

in this scenario also would result in decreases of their nutrient 

components including carbon, nitrogen, and phosphorus 

(tables 7, 8). The stoichiometry used to translate particulate 

organic matter and algae decreases into nutrient decreases was 

estimated based on the algal and organic matter stoichiometry 

used in the calibrated USGS water-quality model. Some 

seasonal variations in these ratios are likely, but currently the 

model allows only one set of values for each compartment.

Concentrations of particulate matter and blue-green 

algae in other inflows, such as the Klamath Straits Drain, 

were unchanged. Water quality in the Klamath Straits Drain 

could be affected by changes in Klamath River water quality, 

because the Klamath Straits Drain is sourced in the Lost 

River basin, and the Lost River basin and Klamath River are 

connected by several canals. For this analysis, however, the 

water quality of the Klamath Straits Drain was assumed to 

be unchanged.
Model Scenarios 25

Results

The model predicted that reduced concentrations of 

algae and particulate matter at Link River would decrease 

algae, chlorophyll a, and particulate matter concentrations 

in the Link-Keno reach (fig. 9; tables A5, A6), causing a 

concomitant decrease in the accumulation of organic matter in 

the sediments in summer. The model also predicted decreased 

concentrations of most dissolved nutrients, including 

orthophosphorus and ammonia, which are released from the 

decay of algae and particulate organic matter. One dissolved 

nutrient, nitrate, was predicted to increase its concentration in 

summer, due to more prevalent oxic conditions. Depending 

on year and modeled treatment, annual average total nitrogen 

and total phosphorus decreased by as much as 19 percent and 

as much as 16 percent, respectively. Because total nitrogen 

and total phosphorus did not decrease equally, the ratio of 

total nitrogen to total phosphorus ratio in the Link-Keno reach 

decreased with this treatment. 

Because decomposing algae and particulate organic 

matter in the water column and sediment exerted high oxygen 

demands over short periods in this study reach (Sullivan and 

others, 2010), a decrease in the amount of this material led 

to overall greater dissolved-oxygen concentrations (figs. 9, 

10; tables A5, A6). Depending on the treatment level, model 

location, and time of year, the effect on dissolved-oxygen 

concentrations could be large, increasing concentrations by as 

much as 4.4 mg/L (153 percent increase) as a June–October 

reach average. There was a short period in late June and 

early July at certain locations where dissolved-oxygen levels 

in near-surface waters were lower with treatment, because 

the algal treatment removed algal oxygen production by 

photosynthesis. However, the overall result of treatment was 

to increase dissolved-oxygen concentrations in the reach. 

Improvement in dissolved oxygen was predicted to occur 

throughout the reach, from the Link River inflow to Keno 

Dam (fig. 10), with notable improvements mid-reach, which 

under base case conditions typically has especially low 

concentration of dissolved oxygen. The effect on dissolved 

oxygen was similar in all 4 years modeled, with a relatively 

linear relation between the load decrease at Link River and the 

increase in dissolved oxygen through the reach (fig. 11).

The pH in the Link-Keno reach was predicted to increase 

after treatment (fig. 9 and tables A5, A6). Total inorganic 

carbon concentrations in the Link-Keno reach decreased due 

to the treatment (fig. 9) because in the CE-QUAL-W2 model 

total inorganic carbon is produced by the decay of particulate 

matter and algae (Cole and Wells, 2008). During periods of 

large algal blooms in Upper Klamath Lake, the Link River 

inflows to the Klamath River have high pH and relatively low 

TIC concentrations because algal photosynthesis consumed 

TIC to create algal biomass. With decreased TIC inputs from 

upstream, and decreased releases of TIC from a smaller load 

of decomposing particulate organic matter in the Link-Keno 

reach, the high pH of the incoming water tended to remain 

high. The release of TIC from decomposition and respiration 

processes was insufficient in these scenarios to replace 

the carbon removed from the inflows; less carbon dioxide 

released means less carbonic acid produced and a greater pH. 

Although most of the treatment effects could be considered 

to be positive, an increase in summer pH could be considered 

a negative effect, because pH levels greater than the Oregon 

maximum pH criterion of 9.0 are undesirable. Because 

ammonia toxicity criteria are pH-dependent in Oregon, the 

criteria would decrease during periods of high pH, although 

the simulated decrease in ammonia concentrations made these 

criteria less likely to be exceeded.

Removing particulate organic matter and blue-green 

algae at Link River for the entire year provided only a small 

improvement over the seasonal treatment from mid-June 

through October (fig. 9, tables A5, A6). For instance, the 

seasonal 90 percent treatment was predicted to increase 

annual volume-average Link-Keno reach dissolved-oxygen 

concentrations by 1.2–1.7 mg/L depending on the year. The 

year-round treatment was predicted to add only an additional 

0.1–0.3 mg/L to the level of improvement (table A5). Most 

Aphanizomenon flos-aquae algae and associated particulate 

organic matter entered the reach in summer and early fall 

(fig. 2) during the period when the seasonal treatment was 

active. The largest benefit occurred for the 90 percent removal 

treatment, compared to 25 or 50 percent removal levels.

Model results also suggest that if Link River particulate 

removal was the selected treatment option, removal of close 

to 90 percent of material, depending on year, may be required 

to bring Link-Keno reach dissolved-oxygen concentrations 

to meet the dissolved-oxygen criteria. For example, in year 

2008, the simulations of June to October 50 percent decrease 

at Link River, still resulted in 30–110 days in which the 

dissolved-oxygen criteria were not attained, depending on 

location. The 90 percent decrease at Link River, however, 

led to dissolved-oxygen criteria being met at all compliance 

locations in that year, except for 6 days at Keno (segment 95).
26 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

tac13-0843_fig 09

0.00

0.04

0.08

0.12

0.16

0.20

0

2

4

6

8

10

0

0.1

0.2

0.3

0.4

0.5

0.6

0.0

0.5

1.0

1.5

0

2

4

6

8

10

12

14

Jan. Mar. May July Sept. Nov. Jan.

2009

Jan. Mar. May July Sept. Nov. Jan.

2009

0

10

20

30

40

6.0

7.0

8.0

9.0

10.0

11.0

Blue-green+POM, in milligrams per liter

Ammonia, in milligrams per liter as N

Orthophosphorus, in milligrams per liter

Nitrate, in milligrams per liter as N

Dissolved oxygen, in milligrams per liter

Total inorganic carbon, in milligrams per liter pH

EXPLANATION

Base case

Scenario 6c, 90 percent, June–October

Scenario 6f, 90 percent, entire year

Figure 9. Simulated water-quality conditions at 1 meter depth at Keno (model segment 95) for the base 

case and for scenario 6 model simulations of 90 percent decrease of particulate organic matter (POM) and 

blue-green algae at Link River, Oregon. Decreases were simulated for the entire calendar year 2009 and 

for June 15–October 31.
Model Scenarios 27

Scenario 7. Route Klamath River Water Through 

Treatment Wetlands

The possible water-quality effects of routing the upper 

Klamath River streamflow through adjacent wetlands and 

then returning the flow back into the river were investigated in 

scenario 7. Wetlands have been hypothesized as a potentially 

effective means of decreasing loads of suspended particulate 

material and nutrients, which could lead to beneficial 

water-quality improvements in the river. In these scenarios, 

only one treatment wetland location was used at a time; in 

the future, simulations of simultaneous operation of multiple 

wetland locations along the river could be considered.

Methods

Wetland Locations

Possible areas for wetland development or restoration 

along the Link-Keno reach were identified by Mahugh and 

others (2008). A subset of the wetlands identified in that report 

were used for the simulations in this report (fig. 12), with the 

simulation of two locations for water withdrawal from the 

Klamath River. The first withdrawal location, for wetland A, 

was at model segment 28 (fig. 12; scenarios 7a-7c). This 

1,400 acre wetland would be located in the Klamath Wildlife 

Area at Miller Island (site 8 in Mahugh and others, 2008). 

The second treatment diversions, for wetlands B, were located 

at model segment 54 upstream of the Klamath Straits Drain 

inflow to the Klamath River (fig. 12; scenarios 7d-7f), and 

incorporated 2,950 acres of possible wetland sites identified 

by Mahugh and others (2008). For all simulations, water was 

assumed to return to the river segment downstream of the 

withdrawal intake location to avoid significant depletion of 

streamflow in the river (table 9). Steady state conditions were 

assumed, with inflows and outflows considered to be equal.

tac13-0843_fig 10

0

2

4

6

8

10

12

105 90 75 60 45 30 15 0

Model segment

Keno Dam

Link River

Dissolved oxygen, in milligrams per liter

EXPLANATION

Flow direction

Scenario

 Base case (2007)

 6a, June-October, 25 percent

 6b, June-October, 50 percent

 6c, June-October, 90 percent

Figure 10. Simulated dissolved-oxygen 

concentration in the Link-Keno reach, Klamath 

River, Oregon on August 1, 2007 under the base 

case and for scenario 6 decreases in Link River 

algae and particulate organic matter. Values 

are daily average, segment volume-average 

concentrations.

Dissolved oxygen increase, in milligrams per liter

0

1

2

3

4

0 2,000 4,000 6,000 8,000

Link River particulate organic matter and 

algae load decrease, in metric tons

2006

2007

2008

2009

EXPLANATION

Figure 11. Relation between Link River 

particulate organic matter and algae load 

decrease and the predicted dissolved oxygen 

increase in the Link-Keno reach, Klamath River, 

Oregon, for each of the years modeled, 2006–09. 

Dissolved oxygen increase is a reach average 

for June to October each year.

Table 9. Wetland representations for scenario 7 simulations, 

Klamath River, Oregon.

[Wetland locations are shown in figure 12]

Wetland Scenario

Approximate

area

(acres)

Diversion 

model 

segment

Return 

model 

segment

A 7a,7b,7c 1,400 28 29

B 7d,7e,7f 2,950 54 55
28 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

tac13-0843_fig 12

2

80

40

60

100

20

Keno Dam

Link River

A

B

Figure 12. CE-QUAL-W2 model grid, location of wetland A and B areas, and approximate diversion and 

return flow points (marked with arrows) for scenario 7 simulations, Klamath River, Oregon.
Model Scenarios 29

Wetland Effects on Water Quality

The water quality of the return flow reflected projected 

changes in water quality after passing through the wetland. 

Removal fractions for total suspended solids (TSS) and BOD 

are typically 60–80 percent for BOD and 50–90 percent for 

TSS depending on the nature and concentration of the influent 

and the flow rate (Crites and Tchobanoglous, 1998). The TSS 

and BOD decreases then were used to modify the relevant 

components of the model input files.

For this analysis, volumetric averages of water 

temperature, BOD, and TSS in the diverted water from 

segments 28 or 54 were calculated from base-case model 

results (scenario 1a) for May 1 through October 31. Three 

different treatment wetland calculator results (Mahugh 

and others, 2008) were used to estimate BOD and TSS 

removal rates, as well as the required wetland area for a 

target BOD removal rate of 50 percent. Other analysis 

assumptions included 

• Wetland diversion flow rate of 100 ft3/s, 

• Wetland depth of 2 ft, and

• Influent water temperature, BOD, and TSS based on 

simulated instream values for segments 28 and 54.

Influent concentrations and wetland calculator results 

are shown in table 10. This analysis assumes that wetland 

diversion flow rates and wetland areas can be increased in 

direct proportion, such that a 400 ft3/s wetland diversion flow 

rate would correspond to a wetland that is four times the area 

listed in table 10.

The treatment wetland tool predicted increases in 

BOD and TSS levels when inflow concentrations were 

low (for example, minimum ranges in table 10). In such 

circumstances, wetland plants and processes can potentially 

produce BOD and TSS levels that are greater than the lowest 

influent concentrations hypothesized from the Klamath 

River. The use of treatment wetlands when river conditions 

are near this lower bound may not be advisable due to low 

removal efficiency.

For these simulations, two sets of model runs were 

completed for two removal rates of BOD and TSS: 50 percent 

(scenarios 7a, 7b, 7d, 7e) and 90 percent (scenarios 7c, 7f). 

BOD and TSS representations in model input were assumed 

to be composed of inorganic suspended sediment (ISS), labile 

particulate organic matter (LPOM), refractory particulate 

organic matter (RPOM), labile dissolved organic matter 

(LDOM), and the three algae types (table 11). Decreases 

in total nitrogen (TN) and total phosphorus (TP) in these 

scenarios would be somewhat less than the specified 50 and 

90 percent decrease rates in actual field conditions because, 

in addition to POM, LDOM, and algae, TN and TP included 

refractory dissolved organic matter (RDOM), ammonia 

(NH4), orthophosphorus (PO4), and nitrate (NO3), which were 

assumed to be unchanged through the wetland. 

Table 10. Wetland calculator results (required wetland area and removal rates) for model segments 28 and 54 of the 

Link-Keno reach for influent maximum, average, and minimum biochemical oxygen demand and total suspended solids per 

100 cubic feet per second of flow diverted to a wetland in the Link-Keno reach of the Klamath River, Oregon.

[Model segments are shown in figure 12. Calculated maximum, average, and minimum values include the 4 years (2006–09), where the 

treatment period was for May 1–October 31 for each year. Range of required area: All removal rates listed are the average of the results of three 

models: (1) RCM model; (2) Declining k model (Crites and Tchobanoglous, 1998), (3) Water budget model (Tchobanoglous and others, 2000). 

Abbreviations: BOD, biochemical oxygen demand; TSS, total suspended solids; na, not applicable; mg/L, milligram per liter; –, no removal]

Model 

segment

Calculated input Wetland tool results

Influent 

BOD 

(mg/L)

Influent 

TSS

(mg/L)

Range of required 

area for 50 percent 

BOD removal 

(acres)

TSS removal 

for identified 

wetland area

(percent)

Average 

(maximum)

BOD removal

(percent)

TSS removal 

at maximum 

BOD removal 

(percent)

28 Maximum 20.38 45.46 128–160 77–80 75 (70–79) 83–85

54 15.96 34.45 135–166 75–78 71 (67–75) 80–82

28 Average 7.88 13.41 1193–208 56–59 51 (47–55) 56–59

54 6.47 10.90 na2 na2 44 (40–47) 48–51

28 Minimum 31.36 45.93 – – – –

54 31.28 44.55 – – – –

1

At minimum water temperature, the maximum BOD removal efficiency was 47 percent.

2

No value is indicated because maximum BOD removal rates are less than 50 percent. 

3

At low BOD concentrations, BOD was not removed from the water. BOD increased.

4

At low TSS concentrations, TSS was not removed from the water. TSS increased.
30 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Table 11. Specified decreases in modeled return flow due 

to removals of biochemical oxygen demand, total suspended 

sediment, total nitrogen, and total phosphorus through treatment 

wetlands for scenario 7 in the Link-Keno reach of the Klamath 

River, Oregon.

[–, no change]

CE-QUAL-W2 modeled constituent

Removal rate 

(percent)

50 90 

ISS Inorganic suspended sediment X X

LPOM Labile particulate organic matter X X

RPOM Refractory particulate organic matter X X

LDOM Labile dissolved organic matter X X

RDOM Refractory dissolved organic matter – –

ALG1 Algae group 1 (blue-greens) X X

ALG2 Algae group 2 (diatoms) X X

ALG3 Algae group 3 (other algae) X X

NH4 Ammonia – –

PO4 Orthophosphorus – –

NO3 Nitrate – –

RDOM concentrations in the inflow and return flow 

from the treatment wetlands were set to be identical because 

interactions with the wetland soils, macrophyte excretion, 

and various decay processes could add RDOM in the 

wetland and counter any removal process for this constituent. 

Because no data were available regarding nutrient cycling 

in wetlands in the project area, the uptake and production 

of inorganic dissolved nutrients through the treatment 

wetlands were assumed to be approximately equal for these 

initial simulations, so no decrease was applied for dissolved 

inorganic nutrients. The actual concentration of dissolved 

inorganic nutrients in wetlands could change, though 

removal and retention behavior varies among different types 

of wetlands (Vymazal, 2007). Water temperature was not 

changed in these simulations.

Although most of the modeled constituents were 

inter-related through the various removal processes (for 

example, assumed BOD, TSS, TN, and TP decreases of 50 

or 90 percent), BOD was assumed to be the highest priority 

parameter in this analysis, because of the direct effect on 

dissolved oxygen. Thus, specifying BOD decreases tended 

to meet the required decreases in TSS, with the exception of 

ISS, and TN and TP where inorganic forms were assumed to 

remain unchanged.

Flow

For each wetland for scenario 7, withdrawals and 

tributaries for the entrance and the exit points, respectively, 

were added to the model. Wetlands were used for the period 

between May 1 and October 31. Performance of treatment 

wetlands depends directly on the life cycle and density of 

vegetation cover, which affects the hydrodynamic and waterquality conditions, and would not be uniform during May 1 

through October 31. For this scenario as a first-cut estimate, 

however, removal rates were assumed to be fixed through the 

treatment period.

Another assumption involved the lateral averaging of 

the CE-QUAL-W2 model. Diversion and return flows for 

the treatment wetlands occur at the channel margins, and 

the conditions at the margins may differ from conditions 

mid-river. As a result, local water-quality conditions in 

the river could be different than that simulated in the 

CE-QUAL-W2 model.

One constraint on the use of treatment wetlands is the 

available water in the Klamath River. Because the Link-Keno 

reach is both a diversion source and return flow destination, 

the flow rate varies at different locations. For instance, 

waters can be diverted from the Klamath River at Lost 

River Diversion Channel (segment 19) and returned through 

Klamath Straits Drain (segment 69) about 9.3 mi downstream. 

Therefore, the flow rate between the point of diversion and the 

location of return flow can be notably decreased, with flow 

rates less than 300 ft3/s at times. Thus, a simple assumption 

of, for example, a 400 ft3/s delivery rate for a treatment 

wetland may not be feasible in summer in the reach between 

the Lost River Diversion Channel and the Klamath Straits 

Drain. To accommodate the flow variability and occasional 

low flow conditions, and representing an upper bound to 

potential treatment wetland prescription (that is, water quality 

improvement), the entire volume of the river was diverted 

from and returned to the subsequent downstream segment 

in these initial scenario runs. An additional withdrawal for 

the entrance and an additional tributary for the exit were 

introduced to the model. Although there would be considerable 

biological issues and facilities costs to treat the entire river 

(for example, fish screens or intake structures) considering 

the high range of flow in the main stem, this approach was 

deemed acceptable for the purposes of assessing the range of 

potential wetland treatment options. As was the practice for 

previous model scenarios, an end-member approach is helpful 

in determining a potential range of outcomes, and adjustments 

based on other factors (including engineering and legal issues) 

can be made with refined model runs in the future.

In addition to treating the entire river flow, a second, 

more representative case was simulated with the diversion 

flow at a 250 ft3/s fixed flow rate for a fixed wetland area 

(scenarios 7b, 7e). A range of flows, rather than a fixed 

flow rate through the season, could have been used in this 

scenario; however, a fixed flow rate of 250 ft3/s was used after 

considering the available streamflow in the Link-Keno reach 

in 2006–09 and the need to minimize changes in the watersurface level of the river. 
Model Scenarios 31

Results

Routing water through wetlands and back into the 

Klamath River in these scenarios produced elevated dissolvedoxygen concentrations and lower chlorophyll a, particulate 

organic carbon, total phosphorus, total nitrogen, ammonia, and 

orthophosphorus concentrations downstream of the wetlands 

(tables A7, A8) compared to the base case. Concentrations of 

nitrate were predicted to increase slightly due to the greater 

levels of dissolved oxygen.

The effect of the wetland occurred only downstream of 

the location where wetland return flows reentered the reach. 

Thus, return flows from wetland A at segment 29 (fig. 12) 

would not affect water quality in upstream segments 2 through 

28. Likewise, return flows from wetland B at segment 55 

would not affect water quality in segments 2 through 54. 

Because the highest concentrations of organic matter and algae 

typically were in the upstream end of the Link-Keno reach, 

there would be lower removal efficiencies in wetlands farther 

downstream in the reach because there would be less material 

to remove. Model results also indicated that the greatest 

dissolved oxygen improvement was not immediately at the 

wetland flow return point, but farther downstream in the LinkKeno reach (fig. 13), mostly because the improvements in 

dissolved oxygen were a result of decreased oxygen demands 

(BOD and sediment oxygen demand), which take time and 

downstream distance to be expressed.

Simulation of 90 percent BOD and TSS removal 

in the wetlands led to more improvements in Klamath 

River water quality compared to simulation of 50 percent 

removal. Changes in water quality with a fixed 250 ft3/s flow 

rate through the wetlands always were less than changes 

achieved by treating the entire flow of the river for the same 

50 percent decrease rate (fig. 13; tables A7, A8). Significant 

improvements in water quality could be made through the 

use of treatment wetlands, but large fractions of the river flow 

would need to be treated to provide the improvements that 

might be needed to meet water-quality criteria. If located in an 

advantageous location in the upstream part of the Link-Keno 

reach, treatment wetlands at some scale may be a useful part 

of a larger program of water-quality improvement.

tac13-0843_fig 13

0

2

4

6

8

10

12

105 90 75 60 45 30 15 0

Model segment

Keno Dam

Link River

0

2

4

6

8

10

12

Dissolved oxygen, in milligrams per liter

EXPLANATION

Base case (2007)

Scenario

7d, segment 54, 50 percent

7e, segment 54, 50 percent, 250 ft3

/s

7f, segment 54, 90 percent

EXPLANATION

Base case (2007)

Scenario

7a, segment 28, 50 percent

7b, segment 28, 50 percent, 250 ft3

/s

7c, segment 28, 90 percent

Flow direction

Figure 13. Simulated dissolved-oxygen 

concentration under the base case and for 

wetland simulations in scenario 7 in the Link-Keno 

reach of the Klamath River, Oregon, August 1, 

2007. Wetlands were simulated at segments 

28 (top graph) and 54 (bottom graph). Values 

are daily average, segment volume-average 

concentrations.
32 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Scenario 8. Altered Flow—Import/

Export to and from the Klamath Project

The objective of model scenario 8 was to 

investigate how different options for importing and 

(or) exporting water to and (or) from Reclamation’s 

Klamath Project through the A Canal, Lost River 

Diversion Channel, and (or) Klamath Straits Drain 

could affect water-quality conditions in the upper 

Klamath River.

Table 12. Flow rates used in scenario 8, Klamath River, Oregon.

[Flow changes were implemented for the period June 15–October 15. Abbreviaton: ft3/s, 

cubic foot per second]

Scenario Link River Lost River 

Diversion Channel

Klamath Straits 

Drain

Base case Base case Base case Base case

8a Base case – 200 ft3/s Base case + 200 ft3/s Base case

8b Base case – 200 ft3/s Base case Base case + 200 ft3/s

8c Base case – 200 ft3/s Base case + 100 ft3/s Base case + 100 ft3/s

Methods

Three model runs were tested to evaluate the effects of 

diverting more water through the Klamath Project and Lost 

River basin rather than down Link River, increasing return 

flows through the Lost River Diversion Channel or Klamath 

Straits Drain by the same amount. The return flows might have 

less particulate material compared to water in Link River, 

thus imparting a potential water-quality benefit to the river. 

The three simulations all decreased Link River inflows by 

200 ft3/s, with that flow diverted into the A Canal, which flows 

into the Lost River basin. The A Canal and Lost River are 

outside the model boundary, so the flow and biogeochemical 

transformations in those reaches were not modeled directly. 

The 200 ft3/s flows were returned to the Klamath River 

through the Lost River Diversion Channel and (or) the 

Klamath Straits Drain (table 12). Flows in these two canals 

originate in the Lost River basin for all or part of the year and 

were included as tributary nonpoint sources in the Link-Keno 

model. The Lost River Diversion Channel operates either as a 

tributary to or withdrawal from the Klamath River, depending 

on time of year. If it was operating to withdraw Klamath River 

water to the Lost River basin, those withdrawal flows were 

decreased by 200 ft3/s, with the consideration that the diverted 

A Canal flows could be used in the Lost River basin in place 

of Lost River Diversion Channel withdrawals.

Flow changes were implemented for June 15 through 

October 31 for each year modeled. Typical flows at Link River 

for this period were 500–3,300 ft3/s in 2006–09, with elevated 

flows in June and lower flows in September–October. Flows 

at Keno Dam were the same in the base case and scenario 

runs, because the flow decrease in Link River was balanced by 

flow increases in Lost River Diversion Channel and Klamath 

Straits Drain.

Routing more flow into the Lost River basin could affect 

the quality of water returned through the return canals, but for 

this initial simulation set, that water quality was assumed to be 

unchanged. Travel time effects on the concentrations in Lost 

River Diversion Channel and Klamath Straits Drain were not 

considered in these initial runs, although travel time effects 

in the Link-Keno reach as a result of decreased flow at Link 

River was considered by the model.

Water returning to the Klamath River through the Lost 

River Diversion Channel would follow a relatively short flow 

path; water returning through Klamath Straits Drain would 

follow a longer return path and be exposed to potentially 

different soils and wetland environments. These differences 

could be taken into account in a follow-up experimental and 

modeling analysis in the future.

Results

Simulated changes in water quality through the LinkKeno reach were dependent on the water quality in the three 

main boundary inflows (Link River, Lost River Diversion 

Channel, and Klamath Straits Drain) under consideration 

in this scenario. For instance, Link River typically had 

high concentrations of algae and particulate organic matter. 

Decreased imported loads of these constituents through Link 

River in these simulations resulted in lower concentrations of 

chlorophyll a and particulate organic matter in the Link-Keno 

reach. Concentrations of chlorophyll a and particulate organic 

matter decreased by about 4–16 percent as a June–October 

entire-reach average, depending on year and scenario.

Routing more return flow through the Klamath Straits 

Drain (scenario 8b) did not reduce ammonia concentrations 

(tables A9, A10); rather, ammonia concentrations tended to 

increase. On the other hand, the models predicted a minor 

decrease in ammonia concentrations when the return flow was 

routed through the Lost River Diversion Channel (scenario 

8a). Nitrate concentrations were similar through these 

simulations, with slight increases in nitrate levels observed 

through the reach for all simulations. Due to relatively high 

orthophosphorus levels in the Klamath Straits Drain and Lost 

River Diversion Channel, none of the options were effective 

in reducing orthophosphorus concentrations. Compared to the 

base case scenario, overall average dissolved-oxygen levels 

did not change significantly through the reach for any of the 

scenario 8 simulations (fig. 14). Most of the improvement in 

dissolved-oxygen conditions occurred downstream of Miller 

Island, probably as a result of decreased oxygen demands 

directly related to decreased loads of particulate material 

imported through Link River. This improvement, however, 
Model Scenarios 33

came at the expense of degraded dissolved-oxygen conditions 

in the more upstream part of the Link-Keno reach, which were 

probably due in part to a longer travel time upstream of Lost River 

Diversion Channel. Longer travel times allow oxygen demands 

more time to be expressed.

Some water-quality changes were due to differences in 

water quality in the various inflows, but some water-quality 

changes were due to internal mixing and travel time effects. As 

an example, at segment 8 in 2007, which is downstream of Link 

River but upstream of Lost River Diversion Channel and Klamath 

Straits Drain, there was an increase in total dissolved solids 

(TDS) concentration (fig. 15), a constituent that is conservative 

in CE-QUAL-W2, with concentrations altered only by 

hydrodynamics or mixing, rather than biogeochemical processes. 

One likely explanation is that with less Link River flow, the model 

input distributed tributary, which has greater TDS, would make up 

a larger part of the flow here. The distributed tributary is a model 

input designed to close the water balance and is meant to represent 

groundwater inputs and ungaged surface water inputs. Some 

travel time effects also were evident, as decreased velocities in the 

upstream part of the model domain accompanied the decreased 

flow at Link River (fig. 15). Decreased velocities allow more time 

for the expression of oxygen demands, which could account for 

the faster loss of dissolved oxygen downstream of Link River in 

scenario 8 simulations compared to the base case (fig. 14).

tac13-0843_fig 14

0

2

4

6

8

10

12

105 90 75 60 45 30 15 0

Model segment

Keno Dam

Link River

Dissolved oxygen, in milligrams per liter

EXPLANATION

Base case (2007)

Scenario

8a, flow to Lost River Diversion Channel (LRDC)

8b, flow to Klamath Straits Drain (KSD)

8c, flow to LRDC and KSD

Flow direction

Figure 14. Simulated dissolved-oxygen 

concentration under the base case and for flow 

routing simulations in scenario 8 in the Link-Keno 

reach of the Klamath River, Oregon, August 1, 

2007. Values are daily average, segment volumeaverage concentrations.

Jan. Mar. May July Sept. Nov. Jan.

2007

Jan. Mar. May July Sept. Nov. Jan.

2007

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

70

80

90

100

0

500

1,000

1,500

2,000

2,500

3,000

0

2

4

6

8

10

12

14

EXPLANATION

Base case

Scenario

8b

60

Flow, in cubic feet per second Velocity, in feet per second

Total dissolved solids, in milligrams per liter Dissolved oxygen, in milligrams per liter

Figure 15. Simulated daily average flow, velocity, total dissolved solids, and dissolved oxygen at segment 

8 for the base case (scenario 1a) and scenario 8b, Klamath River, Oregon, 2007.
34 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Scenario 9. Augment Dissolved Oxygen or Add 

Riparian Shade

The purpose of scenario 9 simulations was to assess water 

quality under different options to increase dissolved oxygen 

and reduce water temperature. These options can be regarded 

as exploratory, because definitive approaches for augmenting 

dissolved oxygen and reducing water temperatures in the 

Link-Keno reach have not yet been developed. Potential 

prescriptions for dissolved-oxygen augmentation include 

reaeration with atmospheric oxygen and direct aqueous 

augmentation. Direct aqueous augmentation is an oxygen 

transfer system where supersaturated water is piped into the 

river. Water temperature changes associated with increasing 

the amount of vegetative riparian shading also was explored.

Methods

Dissolved-Oxygen Augmentation

Two options for augmenting dissolved oxygen were 

considered. A “reaeration” or “saturation dissolved oxygen” 

set of simulations (scenarios 9a, 9b, 9c) assumed that 

dissolved-oxygen concentrations at three selected locations 

(one location in each run) were assumed to reach saturation 

with respect to atmospheric oxygen as a result of some 

reaeration treatment. To model this condition, the whole water 

volume in the river was withdrawn, dissolved-oxygen levels 

set to saturated conditions, and then returned to the river at 

a nearby downstream location. Although annual simulations 

were completed, the saturation dissolved oxygen treatment 

was applied between July 1 and October 31.

In a second set of simulations called “supersaturated” 

(scenarios 9d, 9e, 9f), a fixed rate of flow of 100 ft3/s 

(2.83 m3/s) was withdrawn from the river, supersaturated with 

dissolved oxygen to a concentration of 100 mg/L, and returned 

to the river just downstream of the withdrawal point. This 

supersaturated aqueous injection was set up for three locations 

(one location in each run) during July 1 to October 31. The 

water with 100 mg/L of dissolved oxygen was assumed to be 

injected at depth as outlined below.

For both sets of model runs, three locations were 

selected:

1. Near Railroad Bridge. Withdrawal segment 7, receiving 

segment 9. For supersaturated model runs, water was 

injected into the two layers above the bottom-most 

active layer. 

2. Highway 97. Withdrawal segment 21, receiving 

segment 22. For supersaturated simulations, water was 

injected into the three layers above the bottom-most 

active layer.

3. Miller Island. Withdrawal segment 38, receiving 

segment 39. For supersaturated simulations, water 

was injected to the six layers above the bottom-most 

active layer.

Riparian Shade

In the base case model, topographic and vegetative 

riparian shading were both set to zero because (1) topography 

did not provide any substantial shading and (2) woody riparian 

vegetation of any significant height was limited. Because 

topographic conditions cannot be modified, this scenario 

focused on the effect of increased vegetative riparian shade. 

CE-QUAL-W2 has options to simulate static or dynamic 

shade, where the first is unchanging and the second changes 

with time of day and season. Dynamic shade, as simulated 

here, takes into account factors such as vegetation height and 

density, distance from the river centerline to the controlling 

line of vegetation, sun angles, river segment orientation, and 

the cycles and timing of deciduous vegetation cycles (leaf on 

and leaf off).

For these simulations, deciduous trees were assumed 

to colonize the river edge on the left and right banks for the 

entire Link-Keno reach. Tree heights of 32.8 and 65.6 ft 

(10 and 20 m) were simulated in different model runs. 

Transmission of solar radiation through the canopy was 

assumed to be zero (100 percent solar blockage) during the 

period when the modeled trees had leaves, from late March 

through mid-October. These model runs represent an end 

member condition to examine the maximum potential effects 

of added shade; additional simulations with less vegetation 

could be completed to represent realistic possibilities for 

future vegetation densities, heights, and distributions.

Shading was not considered to affect boundary inflow 

temperatures for the following reasons:

1. Due to the size of Upper Klamath Lake, shade along Link 

River was assumed to have little to no effect on the Link 

River boundary temperature.

2. Lost River Diversion Channel is about 100 ft wide 

from the Lost River to the Klamath River. At 100 ft in 

width, an effective tree height would be in the range 

of 80 to 100 ft and continuous. This degree of riparian 

vegetation height and density are not likely because such 

large trees might endanger levee integrity and access for 

maintenance; typically, riparian vegetation is removed 

from these levees.

3. The Klamath Straits Drain is about 75 ft wide for much of 

its length. Levees also border this system, although they 

are not as high as Lost River Diversion Channel levees. 

Beyond shading the drain properly, the challenge for this 

system would be to shade all the laterals that feed into 

the drain in this reach. Further, the operations of the drain 

and lands adjacent to the drain would need to be known 

and simulated to properly represent water temperatures. 

Additionally, wildlife refuges upstream of the Klamath 

Straits Drain have large areas of open water marshes that 

would be challenging to manage for water temperature.
Model Scenarios 35

Results

Dissolved-Oxygen Augmentation

Both the “saturated” and “supersaturated” scenarios 

were effective at increasing dissolved-oxygen concentrations 

in the Link-Keno reach. The point of maximum effect on 

river dissolved-oxygen concentrations was immediately 

downstream of the saturation or injection point, and the 

effect decreased in the downstream direction as a result of 

consumption by decomposition and respiration processes 

as well as losses to the atmosphere for the supersaturated 

runs (fig. 16). Thus, if a specific location was targeted for 

dissolved oxygen improvement, the model predicts that the 

maximum benefit would be achieved by locating the saturation 

or injection point at or just upstream of that location. This 

differs from the wetland treatment scenarios, where the point 

of greatest dissolved oxygen improvement was some distance 

downstream of the treatment location.

Although these dissolved-oxygen saturation and injection 

treatments were effective at increasing dissolved-oxygen 

concentrations, the model predicted that the effect on other 

water-quality constituents in the reach would be modest 

(tables A11, A12). This scenario did not change the source 

of the low-dissolved-oxygen conditions; it simply addressed 

and masked one of the outcomes by raising dissolved-oxygen 

concentrations. The model did predict minor increases in 

nitrate concentrations under these treatments, which was likely 

because more oxygenated conditions favored that form of 

dissolved nitrogen.

Saturating the water column at Miller Island (segment 38) 

generally improved reach-average June-October dissolvedoxygen concentrations more than saturating the river at the 

two upstream locations (table A12) in the 4 years modeled. 

This likely is because the Miller Island location often has 

some of the lowest dissolved-oxygen concentrations in the 

reach, which allowed the most dissolved oxygen to be added 

through the reaeration process.

In 3 of the 4 years modeled, the supersaturated runs 

indicated that of the three modeled injection locations, the 

site at Highway 97 (segment 21) increased June–October 

dissolved oxygen concentrations in the Link-Keno 

reach by the greatest amount. The simulated maximum 

dissolved-oxygen concentration for the supersaturated 

injection at Miller Island sometimes was greater than the 

maximum results for the other two locations (fig. 16, August 1 

results), probably because river flows at that site were lower, 

because it is downstream of the Lost River Diversion Channel 

withdrawal. The supersaturated scenarios were predicted 

to produce dissolved-oxygen concentrations in excess of 

saturation at the injection location. If this type of treatment 

were used, the Link-Keno model could be used to assist with 

optimizing the treatment specifics to allow the maximum 

benefit, while eliminating excess oxygen treatment when not 

necessary. The model also could be used to help optimize the 

tac13-0843_fig 16

0

2

4

6

8

10

12

105 90 75 60 45 30 15 0

Model segment

Keno Dam

Link River

Dissolved oxygen, in milligrams per liter

EXPLANATION

Scenario

Base case (2007)

9a, segment 7 saturated

9b, segment 21 saturated

9c, segment 38 saturated

9d, segment 7 supersaturated

9e, segment 21 supersaturated

9f, segment 38 supersaturated

Flow direction

Figure 16. Simulated dissolved-oxygen 

concentration under the base case and for 

saturated and supersaturated model runs 

for scenario 9 in the Link-Keno reach of the 

Klamath River, Oregon, August 1, 2007. Values 

are daily average, segment volume-average 

dissolved oxygen concentrations.

reaeration/saturation treatment, because these exploratory runs 

assumed the entire river reaches saturation, although it may 

be more realistic to attain such conditions for only parts of the 

water column or river.

Shading

Even with the simulation of dense 65.6 ft (20 m) trees 

along the entire Link-Keno reach, the predicted cooling effect 

was modest, with an average temperature decrease of less than 

0.6°C through the reach for June–October (table A14). The 

amount of cooling increased from upstream to downstream 

reaches due to the cumulative effect of shade along the entire 

reach (fig. 17). Other water-quality constituents that might be 

affected by shade, and the resulting decreased water temperature 

and less light for photosynthesis, revealed only minor effects in 

these simulations. Average concentrations of dissolved oxygen, 

ammonia, nitrate, chlorophyll a, particulate organic carbon, 

dissolved organic carbon, total nitrogen, total phosphorus, and 

pH were predicted to remain unchanged or to decrease slightly 

(tables A13, A14). Average concentrations of orthophosphorus 

were predicted to increase, but by an insignificant amount.
36 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

The simulation of 65.6 ft (20 m) trees with dense 

canopies along the entire reach was an end member simulation 

used to examine what might be the maximum possible effects 

of vegetative shading. More realistic amounts of possible tree 

density, height, and extent would produce even smaller water 

temperature and water-quality effects. The effect of shade 

on the Link-Keno reach was limited, primarily because the 

relatively wide river channel is much wider than the shade cast 

by vegetation typical to the area.

Scenario 10. Climate Change Effects on 

Water Quality

Scenario 10 explored possible water-quality effects of a 

future warmer climate on the Link-Keno reach. Predicted air 

temperature increases were derived from Global Circulation 

Model (GCM) results, downscaled for the Klamath Basin. 

These predicted future temperatures were used to adjust the 

Link-Keno model meteorological conditions and boundary 

inflow water temperatures.

Methods

Predicted future air temperature changes were derived 

from five future GCM climate scenarios, which were 

simulated as part of a recent Klamath River dam removal 

study (Bureau of Reclamation, 2011; King and others, 2011). 

As part of that study, precipitation and air temperature 

predictions from five GCMs were downscaled to the upper and 

lower Klamath River basin. Hydrologic and meteorological 

conditions were forecast under the different climate change 

scenarios for a future period of 50 years. In the dam removal 

study, the downscaled precipitation and air temperature 

results provided input to a watershed scale hydrologic model, 

SAC-SMA, which estimated future hydrologic runoff to be 

used by two hydrologic decision models. Input hydrology 

for the two decision models was monthly, and daily flows 

were disaggregated for the downstream daily model using 

an approach that matched historical seasonal hydrology. 

The climate and Klamath dam removal study examined 

management alternatives under current operations with 

dams in-place and under the full Klamath Basin Restoration 

Agreement (Klamath Basin Restoration Agreement, 2010) 

with four downstream dams removed; Link and Keno Dams 

would remain in-place.

For this study focusing on the Link-Keno reach of 

the Klamath River, future air temperature, dew point 

temperature, and water temperature of inflows were estimated 

based on the GCM-predicted annual average air temperature 

changes (maximum, median, minimum) between the base 

period 2006–09 and the future period 2057–60. Over 50 years, 

future air temperature was predicted to increase in all GCM 

simulations, although the amount of temperature change 

varied between simulations. The Link-Keno model for 

calendar year 2007 was selected as the base model for this 

scenario, although any of the 4 years could have been used.

Flows

Initial plans for these model runs were to apply the 

hydrologic outputs of the climate change models to the 

Link-Keno CE-QUAL-W2 models. For several reasons, 

however, climate change flows were not used, but base 

scenario conditions (base case) flows were used.

The first reason to retain the base-case flows was that 

hydrologic conditions predicted for the Link-Keno reach were 

relatively similar in current and future years. The dam removal 

study hydrologic results illustrated that year-to-year flow 

differences were often greater than the overall flow change 

from the base case years to the future 50-year period. For 

example, Keno Dam outflows for the CE-QUAL-W2 2006–09 

models were plotted with the 2012–60 monthly flows (fig. 18) 

from one of the downscaled GCM models (Canadian Centre 

for Climate Modeling Analysis, using the 75th precipitation 

quantile; other GCM models that use 50 or 25 percent 

precipitation percentiles would simulate drier years than the 

CCCMA model). The general seasonal patterns in flow were 

similar for the base-case and future years predicted by the 

GCM. On an annual average basis, the range of flows for 

future years 2057–60 and for base years 2006–09 were similar, 

with the range simulated for the entire period of 2012–60 

including both wetter and drier conditions (fig. 19).

tac13-0843_fig 17

105 90 75 60 45 30 15 0

Model segment

Keno Dam

Link River

EXPLANATION

Scenario

22

23

24

25

26

Base case (2007)

9g, 10 meter trees

9h, 20 meter trees

Water temperature, in degrees Celsius

Flow direction

Figure 17. Simulated water temperature under 

the base case and for shading simulations in 

scenario 9 in the Link-Keno reach of the Klamath 

River, Oregon, August 1, 2007. Values are daily 

average, segment volume-average temperatures.
Model Scenarios 37

tac13-0843_fig 18 Flow, in cubic feet per second

Jan. Mar. May July Sept. Nov.

2,000

0

4,000

6,000

8,000

10,000

12,000

EXPLANATION

2006 base case

2007 base case

2008 base case

2009 base case

2012–60, CCCMA flows

Figure 18. Outflows from the CE-QUAL-W2 

base-case model for 2006–09 and from the 

Canadian Centre for Climate Modeling Analysis 

(CCCMA) model for 2012–60 at Keno Dam, 

Klamath River, Oregon.

Flow, in cubic feet per seond

0

500

1.000

1.500

2.000

2.500

3.000

3.500

Base case 2006–09

CCCMA 2057–60

CCCMA 2012–60

EXPLANATION

Figure 19. Annual average outflow at Keno 

Dam, Klamath River, Oregon. Base-case flows 

are compared to future Canadian Centre for 

Climate Modeling Analysis (CCCMA) flows.

Another reason to retain the base-case flows is that 

serious challenges exist in using second-generation hydrologic 

data from a model that had different objectives, and spatial 

and temporal resolution. For instance, the monthly time step 

for flow in the dam removal study (Bureau of Reclamation, 

2011) was much longer than the 30-minute to daily time step 

used for CE-QUAL-W2 input. Additionally, the future flow 

operations model was not used to manage diversions and 

return flows or storage (assumed constant) in the Link-Keno 

reach, but instead was used for long-term planning horizon 

studies at the basin scale. The Link-Keno CE-QUAL-W2 

modeling (Sullivan and others, 2011) focused on a specific 

Table 13. Annual average change in air 

temperature between 2006–09 and 2057–60 from 

five Global Circulation Models for the Klamath 

River basin, Oregon.

Annual average air

temperature change 

(degrees Celsius)

Minimum 0.86

Median 1.99

Maximum 3.25

reach, examining water quality responses on short timescales 

in longitudinal and vertical detail. If future CE-QUAL-W2 

climate change scenarios include altered flows, consideration 

of these smaller-scale hydrologic conditions will be important 

before using hydrologic results from available climate change 

models. For these reasons, this climate change analysis 

focuses only on the effects of air temperature change and the 

related meteorological and water-quality changes. 

Meteorological Conditions

Using output from all five GCMs, a minimum, median, 

and maximum annual average air temperature change for 

the Link-Keno reach was determined between 2006–09 and 

2057–60 (table 13). Three model runs were constructed by 

increasing the measured hourly air temperatures for the LinkKeno reach for 2007 by these minimum (10a), median (10b), 

and maximum (10c) annual average air temperature changes. 

For these three runs, the dew point temperature for model 

input was recalculated assuming that relative humidity would 

remain unchanged in the future period, and air temperature 

was increased by the minimum, median, and maximum 

changes. For the base-case year 2007, relative humidity was 

calculated using dew point temperature and air temperature 

inputs. These dew point temperature calculations used 

equations from Snyder and Shaw (1984):

( )

( )

17.27 / 237.3

( ) /100

6.108

ln /17.27

6.108

237.3 / 1

where

is saturation vapor pressure (millibar), 

is dry-bulb air temperature (degrees Celsius),

is vapor pressure (millibar),

is 

s

T T

s

s

E RH E

E e

E B

D BB

E

T

E

RH

+

= ×

=

  =    

= −

relative humidity (percent), and

D is dew point temperature (degrees Celsius). 

(1)
38 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Water Quality

Water temperature boundary conditions were updated 

after the meteorological changes were implemented. 

Procedures similar to those used by Perry and others (2011) 

were applied, with use of the Mohseni equation (Mohseni 

and others, 1998) to predict future water temperature. First, 

weekly average air temperatures for the entire reach and 

weekly average water temperature for Link River, Lost River 

Diversion Channel, and Klamath Straits Drain were calculated, 

consistent with the Mohseni equation. Subsequently, the 

weekly average air and water temperatures for the base case 

years were used to develop individual Mohseni equation 

parameters for each inflow:

( ) 1

where

is the weekly mean water temperature, 

in degrees Celsius, 

is the minimum water temperature,

is the maximum water temperature,

is the air temperature at the point of inflection,

a s T

T

e

T

γ β−

α−μ =μ+

+

μ

α

β

γ represents the slope at the inflection point, and

is the weekly mean air temperature, in 

degrees Celsius.

Ta

(2)

Table 14. Final parameter estimates of the non-linear regression model for 

major inputs at selected sites in the Link-Keno reach of the Klamath River, 

Oregon, 2006–09.

[From Mohseni and others, 1998. Temperature values are in degrees Celsius. α, minimum 

water temperature. β, air temperature at the point of inflection. γ, slope at the inflection point]

Boundary or source Limb α β γ

Link River Rising, falling 24.6 9.2 0.199

Lost River Diversion Channel Rising, falling 24.3 8.5 0.201

Klamath Straits Drain Rising 25.4 8.1 0.219

Falling 26.2 9.8 0.192

Similar to Perry and others (2011), the parameter μ was 

set to 0°C and then α, β, and γ were estimated by a non-linear 

regression method for Link River, Lost River Diversion 

Channel, and Klamath Straits Drain using data from the basecase years 2006–09. Separate equations and Mohseni parameters 

were fit to the rising and falling limb time periods, the part of the 

year when air temperature tends to increase or decrease, for each 

of the three locations. For example, in 2007, air temperature 

generally increased through early July and decreased thereafter. 

After obtaining the best-fit parameters from the nonlinear 

regression model, measured weekly mean water temperature was 

plotted against weekly mean air temperature along with results 

from the fitted Mohseni equations for the rising and falling limbs 

of air temperature for the three locations. The fitted equations for 

the rising and falling limbs were quite similar for the Link River 

and Lost River Diversion Channel, so a single equation was used 

for those boundaries (table 14, fig. 20).

After the Mohseni equations were derived for Link River, 

Lost River Diversion Channel and Klamath Straits Drain, future 

weekly averaged water temperatures were estimated using the 

estimated future air temperature. To obtain future hourly water 

temperature, the difference between weekly averaged base 

year water temperature and weekly averaged future year water 

temperature was added to or subtracted from the base year 

hourly water temperatures.

Considering anthropogenic influence on point sources and 

their relatively small flows, water temperature for point sources 

were not estimated for the future years. Base-case values for 

those sources were used in these climate change scenarios.
Model Scenarios 39

tac13-0843_fig 20

0

4

8

12

16

20

24

28

-12 -8 -4 0 4 8 12 16 20 24 28

Water temperature, in degrees Celsius

0

4

8

12

16

20

24

28

Water temperature, in degrees Celsius

Air temperature, in degrees Celsius

Link River

EXPLANATION

Measured

Fitted

EXPLANATION

Measured

Fitted

EXPLANATION

Lost River Diversion Channel

Klamath Straits Drain

Measured, falling limb

Fitted, falling limb

Measured, rising limb

Fitted, rising limb

0

4

8

12

16

20

24

28

Water temperature, in degrees Celsius

Figure 20. Measured weekly mean water 

temperature versus measured weekly mean air 

temperature, with the final fitted equation for the 

entire simulation period (2006–09) for Link River, 

Lost River Diversion Channel, Klamath Straits 

Drain, Klamath River, Oregon.

Results

Water temperatures in the Link-Keno reach consistently 

increased under the warmer future climate condition scenario. 

In summer, the trend of increasing water temperature was 

expressed throughout the entire Link-Keno reach (fig. 21). 

The minimum (10a) air temperature increase of 0.86°C with 

associated dew point temperature and inflow water temperature 

changes led to an annual average water temperature increase 

of 0.6°C for the Link-Keno reach as an annual volume-average 

result (table A15). The median (10b) air temperature increase of 

1.99°C led to an annual average water temperature increase of 

1.4°C. The maximum (10c) air temperature increase of 3.25°C 

led to a water temperature increase of 2.4°C. These increases 

in water temperature could increase risks to key threatened and 

endangered fish species, depending on the time of year.

Because dissolved-oxygen solubility decreases with 

increased water temperature, dissolved-oxygen concentrations 

were decreased under a warmer future condition, as much as 

0.3 mg/L as an annual volume-average under the conditions 

examined here. Model results revealed only minor changes in 

other water-quality constituents (tables A15, A16).

Scenario 10 focused on direct effects of temperature 

changes in the Link-Keno reach. Climate change also could 

affect water-quality conditions and phytoplankton composition 

of Upper Klamath Lake and Lost River watersheds, thus 

changing the inflow water quality of Link River, Lost River 

Diversion Channel, and Klamath Straits Drain. Water quality of 

inflows was not adjusted in this study, except for temperature. 

Future model scenarios could explore how other possible climate 

change effects could affect water quality in the Link-Keno reach.

105 90 75 60 45 30 15 0

Model segment

Keno Dam

Link River

EXPLANATION

Scenario

22

28

Water temperature, in degrees Celsius

23

24

25

26

27

Base case (2007)

10a, minimum

10b, median

10c, maximum

Flow direction

Figure 21. Simulated water temperature under 

the base case and climate warming simulations 

in scenario 10 for the Link-Keno reach of the 

Klamath River, Oregon, August 1, 2007. Values are 

daily average, segment volume-average water 

temperatures.
40 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Overview of Scenario 

Results

Ten sets of scenarios (table 2) 

were tested with the Link-Keno 

water-quality model to provide 

insights into potential water-quality 

changes as a result of changes 

in operational or management 

strategies. Each scenario 

evaluated here affected water 

quality in different ways (fig. 22, 

appendix A). 

Scenarios 1 to 3 assessed the 

water-quality effects of meeting 

TMDL allocations and targets 

and were not associated with 

specific treatments or prescriptions. 

Rather these simulations explored 

systematically decreasing input 

concentrations of dissolved and 

particulate nutrients, organic 

matter, and algae until targets or 

allocations were met. These were 

the only scenarios that resulted in 

large decreases in dissolved organic 

matter (represented as DOC) in 

the Link-Keno reach, especially 

scenarios 2a and 2b (fig. 22). 

Whether the levels of dissolved 

organic matter decreases assumed 

for these simulations are possible 

in this reach is uncertain, given 

that upstream watersheds have 

wetlands that typically have high 

concentrations of dissolved organic 

matter. These TMDL scenarios 

and analyses assessing whether 

water-quality criteria would be 

achieved could be revisited in the 

future when or if specific treatment 

options to meet TMDLs are 

identified for evaluation. 

Scenario 5 evaluated 

particulate shunting, and 

simulated a significant decrease 

in water-quality conditions in 

the Link-Keno reach. However, 

eliminating particulate material 

from the Lost River basin may 

improve water quality there, which 

could be explored in the future 

through additional monitoring, 

research, and modeling. Scenario 6 

simulations focused on removal 

tac13-0843_fig 22

TMDL Shunt LinkR Wetland Flow Oxygen Shade Climate

-all

TMDL

-UKL

TMDL

-trib

Base case

Scenario: 1a 1b 2a 2b 998765 10

17

18

19

20

21

1

3

5

7

9

0

0.2

0.4

0.6

0.8

0

50

100

150

0

2

4

6

8

0

0.1

0.2

0.3

0

1

2

3

4

2

4

6

8

10

12

Water temperature,

degrees Celsius

Dissolved oxygen,

in milligrams per liter

Ammonia,

in milligrams per liter

Chlorophyll a,

in micrograms per liter

Particulate organic carbon,

in milligrams per liter

Dissolved organic carbon,

in milligrams per liter

Total phosphorus,

in milligrams per liter

Total nitrogen,

in milligrams per liter

Figure 22. Simulated water quality for scenarios 1, 2, 5, 6, 7, 8, 9 and 10 for the Link-Keno 

reach of the Klamath River, Oregon. Values are entire-reach averages for June–

October 2007. The horizontal dashed line represents a reference line equal to results from 

the base case.
Future Application and Development 41

of particulate matter and algae at Link River and illustrated 

improvements in dissolved oxygen and other water-quality 

constituents in downstream reaches. The large improvements 

resulting from 90 percent removal of algae and particulate 

matter in Link River demonstrated the importance of that 

inflow to water quality in the Link‐Keno reach. Scenario 7 

examined the effects of wetlands on water quality, addressing 

not only particulate matter and algae in the Link-Keno reach, 

but also changes to ancillary constituents, such as dissolved 

nutrients and oxygen (fig. 22). Scenario 8 examined the 

effects of flow routing changes. Scenario 9 assessed specific 

prescriptions aimed at improving dissolved-oxygen levels 

through mechanical means and water temperature effects 

related to riparian shading. Dissolved oxygen additions 

increased dissolved-oxygen concentrations, but had little 

to no effect on other water-quality constituents in the study 

reach (fig. 22). Riparian shading had little impact on water 

temperatures due to the wide river channel compared to the 

height of native trees that would potentially grow along Keno 

Reservoir. Scenario 10 demonstrated potential changes to 

the Link-Keno reach under a future warmer climate. If warm 

water temperatures remain an issue in the Klamath River, 

alternate management strategies to provide microhabitats with 

cool-water refugia may be useful.

The details of model scenario set-up have direct 

implications on model results. Because specific details of 

water-quality prescriptions and management strategies for this 

reach have not yet been determined, many of these simulations 

were exploratory, examining the range of effects and analyzing 

general temporal and spatial patterns. These results and the 

existing model can be used to assist in assessing, prioritizing, 

and selecting management or treatment options as well as 

helping to refine specific plans.

Future Application and Development

The initial application of the Link-Keno models have 

provided insight into water quality and hydrodynamic effects 

that may occur under various management options or other 

system changes. Based on the results of this modeling study, 

suggestions for future study in this reach include:

Further development of existing scenarios. Selected 

existing scenarios could be developed in more detail based 

on findings to date. For example, the wetland scenario 

(scenario 7) could be formulated to explicitly incorporate a 

wetland into the model grid. This would allow the simulation 

of macrophyte growth, water evaporation, organic matter 

settling, and chemical transformation in the wetland, among 

other benefits. Additionally, some initial scenarios were 

set up in exploratory form, using end-member situations to 

identify possible effects. As more specific restoration plans 

are targeted, scenarios could be updated or reformulated to 

provide insight toward optimizing the water-quality effects 

of particular options. Scenarios could be post-processed 

to provide output in format for specific purposes, such as 

for comparison to water-quality standards or to aquatic life 

habitat metrics.

Additional scenario applications. The scenarios presented 

in this report represent an initial selection of options for 

possible change to the system. There are other management 

and treatment options that could be considered. These might 

include, but are not limited to, changes to the water quality 

or flow at Link River, timing of flows through the Lost River 

Diversion Channel or Klamath Straits Drain, treatment 

options from a recent pollutant reduction workshop (Stillwater 

Sciences and others, 2012), or other management options that 

come under consideration in the future.

Connect to research and modeling on Upper Klamath 

Lake. The outflow of Upper Klamath Lake through Link 

River has a dominant effect on the water quality of this reach. 

Some changes to the Link River inflow are straightforward 

to model with the Link-Keno model, for instance removal 

of particulate matter and algae at Link River (scenario 6). 

However, the water-quality effects of entire-watershed 

changes to Upper Klamath Lake, outside the Link-Keno model 

boundary, are not easy to project. Work is ongoing to improve 

water-quality modeling capabilities for Upper Klamath Lake. 

As model scenarios to examine future conditions in Upper 

Klamath Lake are developed, those results could be used 

in the Link-Keno model to examine how changes in Upper 

Klamath Lake could affect the Link-Keno reach and to provide 

a boundary condition for modeling downstream of Keno Dam. 

Expanding the Link-Keno model to include the 1-mi Link 

River reach would allow a more direct connection to Upper 

Klamath Lake models.

Connect to research and modeling in the Lost River 

basin. The Link-Keno reach is interconnected with the Lost 

River basin through multiple canals. Work to collect data and 

understand processes in the Lost River is ongoing. As results 

from that work become available, the Link-Keno scenarios 

could be updated or expanded to incorporate that knowledge.

Continue selected field work for model improvements.

Although major field work for the purposes of development 

of the 4 years of models is complete, continuing field 

and experimental work could be considered to improve 

understanding of certain water-quality processes. Such field 

work could include experimental work to better understand 

algal health, particulate matter, and nutrient dynamics in the 

Link-Keno reach. Additionally, grab water-quality samples 

in the Link River reach would support expansion of the 

model into this river reach, for ultimate connection to Upper 

Klamath Lake modeling efforts. Although 4 years of model 

results represent a range of flow and climate conditions, field 

sampling in a year with unusual operations, or climatic or 

hydrologic conditions (dry, wet, warm, or cold) would provide 

data to further develop the model and assist in understanding 

the response of the reach to extreme or unusual conditions.
42 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon

Acknowledgments

Funding for this project was provided by the Bureau 

of Reclamation. Discussions with Rick Carlson and Jason 

Cameron at the Bureau of Reclamation were helpful 

during scenario development. Daniel Turner of the Oregon 

Department of Environmental Quality provided helpful 

explanations of the State of Oregon water-quality criteria.

Supplementary Materials

Previous project reports and data along with the 

calibrated base-case models used in this study can be 

accessed at the project web site, http://or.water.usgs.gov/proj/

keno_reach/.

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Appendix A. Volume-Average Annual and June–October 

Scenario Results for the Link-Keno Reach, Upper Klamath 

River, Oregon
46 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon Table A1. Scenarios 1 and 2 annual volume-average results for the Link-Keno reach of the Klamath River, Oregon. [2007 runs were bracketed by also using total inorganic carbon calculated with pH during low-bloom conditions (leftmost values when a range is given for the Link River, Lost River Diversion Channel, and Klamath Straits Drain inputs. Other years were run without modifying the pH of boundary inputs. The effects of recalculating total inorganic carbon with low-bloom pH values were manifested only in the simulated pH and in no other simulated constituents in the Link-Keno reach. Abbreviations: TMDL, total maximum daily load; °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter] Scenario Annual in-reach volume average Water temperature (°C) Dissolved oxygen (mg/L) pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L) 2006 1a Base case 11.2 7.91 8.12 0.398 0.161 0.078 41.1 1.72 8.25 0.165 1.84 15.5 1b Sources at TMDL allocations 11.2 8.00 8.15 0.368 0.093 0.044 38.4 1.54 7.24 0.120 1.59 13.7 2a Link River at TMDL target 11.2 9.08 8.41 0.294 0.166 0.050 14.6 0.70 3.97 0.091 1.06 7.1 2b Link River and sources at TMDL 11.2 9.18 8.46 0.263 0.097 0.016 11.6 0.51 2.96 0.046 0.81 5.4 2007 1a Base case 11.8 7.60 7.97 0.531 0.204 0.076 36.5 1.84 8.22 0.163 2.03 17.0 1b Sources at TMDL allocations 11.8 7.68 7.99–7.99 0.513 0.183 0.048 35.2 1.73 7.47 0.128 1.88 15.6 2a Link River at TMDL target 11.8 9.00 8.10–8.35 0.395 0.212 0.043 11.0 0.65 3.49 0.079 1.14 6.7 2b Link River and sources at TMDL 11.8 9.07 8.13–8.40 0.376 0.190 0.015 9.4 0.53 2.73 0.044 0.99 5.5 2008 1a Base case 11.2 6.75 8.06 0.626 0.199 0.073 32.9 2.54 7.97 0.164 2.17 23.7 1b Sources at TMDL allocations 11.2 6.82 8.09 0.600 0.178 0.045 31.3 2.39 7.13 0.128 2.00 21.2 2a Link River at TMDL target 11.2 8.35 8.45 0.528 0.211 0.047 12.2 0.96 4.06 0.091 1.38 9.2 2b Link River and sources at TMDL 11.2 8.43 8.51 0.501 0.188 0.019 10.3 0.81 3.23 0.054 1.21 7.1 2009 1a Base case 11.4 6.95 8.03 0.518 0.159 0.061 22.9 2.67 7.08 0.145 1.93 23.3 1b Sources at TMDL allocations 11.4 7.01 8.05 0.506 0.152 0.037 22.1 2.54 6.40 0.115 1.81 21.4 2a Link River at TMDL target 11.4 8.64 8.43 0.436 0.176 0.039 7.9 0.89 3.30 0.075 1.15 8.2 2b Link River and sources at TMDL 11.4 8.71 8.46 0.423 0.169 0.015 6.9 0.76 2.62 0.045 1.02 6.6
Appendix A 47

Table A2. Scenarios 1 and 2 June through October volume-average results for the Link-Keno reach of the Klamath River, Oregon. [2007 runs were bracketed by also using total inorganic carbon calculated with pH during low-bloom conditions (leftmost values when a range is given for the Link River, Lost River Diversion Channel, and Klamath Straits Drain inputs. Other years were run without modifying the pH of boundary inputs. The effects of recalculating total inorganic carbon with low-bloom pH values were manifested only in the simulated pH and in no other simulated constituents in the Link-Keno reach. Abbreviations: TMDL, total maximum daily load; °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

June through October in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 18.9 4.42 8.34 0.458 0.060 0.105 84.1 3.12 10.6 0.224 2.27 18.7

1b Sources at TMDL allocations 18.9 4.60 8.39 0.436 0.051 0.073 81.2 2.97 9.51 0.181 2.09 17.1

2a Link River at TMDL target 18.9 6.81 8.91 0.225 0.073 0.054 28.4 1.10 4.77 0.105 1.05 6.4

2b Link River and sources at TMDL 18.9 6.99 8.99 0.199 0.061 0.021 24.8 0.95 3.72 0.062 0.86 5.0

2007

1a Base case 18.5 4.60 8.18 0.566 0.071 0.121 85.0 3.51 11.0 0.247 2.50 24.4

1b Sources at TMDL allocations 18.5 4.70 8.20–8.21 0.549 0.065 0.090 82.9 3.41 10.3 0.208 2.37 23.0

2a Link River at TMDL target 18.5 7.62 8.27–8.94 0.232 0.091 0.055 25.0 1.16 4.51 0.105 1.05 6.7

2b Link River and sources at TMDL 18.5 7.72 8.32–9.00 0.212 0.083 0.024 22.2 1.05 3.71 0.066 0.91 5.8

2008

1a Base case 18.7 3.17 8.43 0.448 0.044 0.093 67.0 4.61 9.65 0.217 2.32 34.0

1b Sources at TMDL allocations 18.7 3.26 8.47 0.426 0.040 0.066 65.1 4.53 8.92 0.183 2.19 31.4

2a Link River at TMDL target 18.7 6.51 9.24 0.220 0.072 0.050 23.8 1.51 4.36 0.101 1.05 9.5

2b Link River and sources at TMDL 18.7 6.63 9.32 0.195 0.064 0.023 21.3 1.42 3.63 0.067 0.91 7.6

2009

1a Base case 18.4 2.85 8.18 0.463 0.067 0.081 43.3 5.08 7.95 0.194 2.20 32.6

1b Sources at TMDL allocations 18.4 2.92 8.20 0.453 0.067 0.059 42.7 5.00 7.50 0.168 2.12 30.5

2a Link River at TMDL target 18.5 6.44 9.01 0.264 0.111 0.040 14.3 1.51 3.32 0.082 1.00 8.0

2b Link River and sources at TMDL 18.5 6.55 9.05 0.252 0.110 0.019 13.2 1.43 2.86 0.056 0.91 6.6
48 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon Table A3. Scenario 5 annual volume-average results for the Link-Keno reach of the Klamath River, Oregon.

[Abbreviations: LRDC, Lost River Diversion Channel; KSD, Klamath Straits Drain; OM, organic matter; DO, dissolved oxygen; °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

Annual in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 11.2 7.91 8.12 0.398 0.161 0.078 41.1 1.72 8.25 0.165 1.84 15.55a Shunt, LRDC and KSD current 11.2 7.06 7.96 0.456 0.151 0.082 55.6 2.49 8.31 0.176 1.99 25.25b Shunt, LRDC and KSD intermediate 11.2 7.07 7.97 0.453 0.150 0.080 55.3 2.47 8.17 0.172 1.97 24.95c Shunt, LRDC and KSD zero OM, 

nutrients and algae, DO at saturation

11.2 7.37 8.05 0.426 0.080 0.060 52.7 2.31 7.23 0.143 1.73 22.4

2007

1a Base case 11.8 7.60 7.97 0.531 0.204 0.076 36.5 1.84 8.22 0.163 2.03 17.0

5a Shunt, LRDC and KSD current 11.8 6.43 7.78 0.607 0.189 0.080 54.9 2.97 8.33 0.179 2.25 35.15b Shunt, LRDC and KSD intermediate 11.8 6.44 7.79 0.605 0.188 0.079 54.7 2.96 8.24 0.177 2.23 34.9

5c Shunt, LRDC and KSD zero OM, 

nutrients and algae, DO at saturation

11.8 6.67 7.85 0.584 0.155 0.066 53.2 2.85 7.42 0.156 2.06 32.4

2008

1a Base case 11.2 6.75 8.06 0.626 0.199 0.073 32.9 2.54 7.97 0.164 2.17 23.7

5a Shunt, LRDC and KSD current 11.2 5.58 7.88 0.676 0.185 0.076 49.0 4.40 8.07 0.184 2.46 59.0

5b Shunt, LRDC and KSD intermediate 11.2 5.58 7.88 0.674 0.184 0.075 48.8 4.39 7.97 0.182 2.44 58.7

5c Shunt, LRDC and KSD zero OM, 

nutrients and algae, DO at saturation

11.2 5.89 7.93 0.648 0.151 0.061 47.0 4.25 7.07 0.160 2.25 54.2

2009

1a Base case 11.4 6.95 8.03 0.518 0.159 0.061 22.9 2.67 7.08 0.145 1.93 23.3

5a Shunt, LRDC and KSD current 11.3 5.88 7.87 0.553 0.143 0.063 34.2 4.73 7.14 0.166 2.22 58.8

5b Shunt, LRDC and KSD intermediate 11.3 5.88 7.88 0.550 0.142 0.061 34.0 4.72 7.03 0.163 2.20 58.5

5c Shunt, LRDC and KSD zero OM, 

nutrients and algae, DO at saturation

11.3 6.04 7.94 0.532 0.114 0.050 33.0 4.60 6.32 0.145 2.05 55.4
Appendix A 49

Table A4. Scenario 5 June through October volume-average results for the Link-Keno reach of the Klamath River, Oregon.[Abbreviations: LRDC, Lost River Diversion Channel; KSD, Klamath Straits Drain; OM, organic matter; DO, dissolved oxygen; °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

June through October in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 18.9 4.42 8.34 0.458 0.060 0.105 84.1 3.12 10.6 0.224 2.27 18.7

5a Shunt, LRDC and KSD current 18.8 2.75 7.97 0.587 0.033 0.113 119.5 5.00 10.7 0.250 2.64 37.5

5b Shunt, LRDC and KSD intermediate 18.8 2.77 7.99 0.581 0.033 0.108 118.7 4.97 10.4 0.242 2.59 37.0

5c Shunt, LRDC and KSD zero OM, 

nutrients and algae, DO at saturation

18.8 2.95 8.03 0.570 0.030 0.096 116.3 4.85 9.58 0.222 2.45 34.3

2007

1a Base case 18.5 4.60 8.18 0.566 0.071 0.121 85.0 3.51 11.0 0.247 2.50 24.4

5a Shunt, LRDC and KSD current 18.5 2.34 7.79 0.741 0.036 0.131 130.0 6.14 11.3 0.283 3.02 62.5

5b Shunt, LRDC and KSD intermediate 18.5 2.35 7.80 0.737 0.035 0.128 129.8 6.12 11.2 0.279 2.99 62.2

5c Shunt, LRDC and KSD zero OM, 

nutrients and algae, DO at saturation

18.5 2.50 7.82 0.725 0.032 0.116 127.4 6.02 10.4 0.259 2.86 59.0

2008

1a Base case 18.7 3.17 8.43 0.448 0.044 0.093 67.0 4.61 9.65 0.217 2.32 34.0

5a Shunt, LRDC and KSD current 18.7 1.64 8.09 0.541 0.021 0.098 105.4 9.14 9.91 0.264 3.01 100.4

5b Shunt, LRDC and KSD intermediate 18.7 1.64 8.10 0.536 0.020 0.096 105.1 9.13 9.74 0.260 2.98 99.9

5c Shunt, LRDC and KSD zero OM, 

nutrients and algae, DO at saturation

18.7 1.71 8.12 0.524 0.018 0.085 103.1 9.05 9.02 0.242 2.86 94.7

2009

1a Base case 18.4 2.85 8.18 0.463 0.067 0.081 43.3 5.08 7.95 0.194 2.20 32.6

5a Shunt, LRDC and KSD current 18.4 1.45 7.91 0.533 0.036 0.085 67.0 9.94 8.11 0.242 2.88 97.4

5b Shunt, LRDC and KSD intermediate 18.4 1.45 7.92 0.529 0.035 0.082 66.8 9.92 7.95 0.238 2.86 96.9

5c Shunt, LRDC and KSD zero OM, 

nutrients and algae, DO at saturation

18.4 1.52 7.93 0.520 0.035 0.076 66.1 9.86 7.58 0.228 2.79 93.2
50 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon Table A5. Scenario 6 annual volume average results for the Link-Keno reach of the Klamath River, Oregon.

[Abbreviations: °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

Annual in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 11.2 7.91 8.12 0.398 0.161 0.078 41.1 1.72 8.25 0.165 1.84 15.5

6a 25 percent decrease, June–October 11.2 8.25 8.19 0.368 0.163 0.077 34.3 1.46 8.23 0.161 1.77 13.3

6b 50 percent decrease, June–October 11.2 8.59 8.26 0.336 0.165 0.076 27.2 1.20 8.20 0.158 1.71 11.2

6c 90 percent decrease, June–October 11.2 9.13 8.36 0.279 0.166 0.074 14.5 0.74 8.16 0.151 1.59 8.0

6d 25 percent decrease, entire year 11.2 8.29 8.19 0.366 0.163 0.077 33.4 1.39 8.23 0.161 1.76 12.4

6e 50 percent decrease, entire year 11.2 8.67 8.27 0.332 0.165 0.076 25.4 1.05 8.20 0.156 1.69 9.5

6f 90 percent decrease, entire year 11.2 9.27 8.39 0.273 0.166 0.074 11.3 0.48 8.16 0.149 1.55 5.1

2007

1a Base case 11.8 7.60 7.97 0.531 0.204 0.076 36.5 1.84 8.22 0.163 2.03 17.0

6a 25 percent decrease, June–October 11.8 7.95 8.04 0.495 0.208 0.074 30.0 1.56 8.19 0.159 1.95 14.3

6b 50 percent decrease, June–October 11.8 8.31 8.13 0.456 0.210 0.073 23.0 1.28 8.15 0.155 1.88 12.0

6c 90 percent decrease, June–October 11.8 8.87 8.27 0.383 0.212 0.071 9.80 0.78 8.10 0.148 1.73 9.0

6d 25 percent decrease, entire year 11.8 8.00 8.06 0.495 0.208 0.074 29.8 1.48 8.19 0.159 1.94 13.2

6e 50 percent decrease, entire year 11.8 8.42 8.16 0.455 0.211 0.073 22.7 1.12 8.16 0.154 1.86 9.9

6f 90 percent decrease, entire year 11.8 9.08 8.32 0.380 0.212 0.071 9.14 0.49 8.10 0.146 1.69 5.3

2008

1a Base case 11.2 6.75 8.06 0.626 0.199 0.073 32.9 2.54 7.97 0.164 2.17 23.7

6a 25 percent decrease, June–October 11.2 7.18 8.14 0.599 0.204 0.072 27.7 2.12 7.94 0.159 2.09 19.1

6b 50 percent decrease, June–October 11.2 7.64 8.25 0.568 0.208 0.070 22.3 1.71 7.91 0.154 2.01 15.8

6c 90 percent decrease, June–October 11.2 8.43 8.41 0.508 0.211 0.068 12.0 1.03 7.87 0.145 1.86 12.2

6d 25 percent decrease, entire year 11.2 7.24 8.15 0.599 0.204 0.072 27.6 2.01 7.94 0.158 2.08 17.4

6e 50 percent decrease, entire year 11.2 7.78 8.27 0.567 0.208 0.070 22.0 1.49 7.91 0.152 1.98 12.6

6f 90 percent decrease, entire year 11.2 8.68 8.46 0.505 0.211 0.068 11.5 0.63 7.87 0.142 1.81 6.6

2009

1a Base case 11.4 6.95 8.03 0.518 0.159 0.061 22.9 2.67 7.08 0.145 1.93 23.3

6a 25 percent decrease, June–October 11.4 7.37 8.11 0.498 0.166 0.059 19.8 2.20 7.06 0.140 1.85 19.8

6b 50 percent decrease, June–October 11.4 7.84 8.20 0.473 0.172 0.058 16.6 1.75 7.04 0.135 1.77 14.8

6c 90 percent decrease, June–October 11.4 8.69 8.36 0.426 0.177 0.056 10.4 1.01 7.01 0.126 1.63 10.7

6d 25 percent decrease, entire year 11.4 7.44 8.12 0.496 0.166 0.059 19.4 2.08 7.06 0.139 1.83 16.9

6e 50 percent decrease, entire year 11.4 8.01 8.24 0.470 0.172 0.058 15.6 1.50 7.04 0.132 1.74 12.0

6f 90 percent decrease, entire year 11.4 8.98 8.42 0.419 0.177 0.056 8.6 0.57 7.01 0.122 1.57 5.9
Appendix A 51

Table A6. Scenario 6 June through October volume average results for the Link-Keno reach of the Klamath River, Oregon.[Abbreviations: °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

June through October in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 18.9 4.42 8.34 0.458 0.060 0.105 84.1 3.12 10.6 0.224 2.27 18.7

6a 25 percent decrease, June–October 18.9 5.15 8.50 0.390 0.066 0.103 66.9 2.46 10.5 0.215 2.12 14.4

6b 50 percent decrease, June–October 18.9 5.89 8.67 0.315 0.070 0.100 48.8 1.78 10.4 0.206 1.95 10.5

6c 90 percent decrease, June–October 18.9 7.05 8.90 0.181 0.074 0.096 16.5 0.62 10.3 0.192 1.66 4.6

6d 25 percent decrease, entire year 18.9 5.18 8.51 0.389 0.066 0.102 66.8 2.45 10.5 0.215 2.12 14.1

6e 50 percent decrease, entire year 18.9 5.95 8.68 0.313 0.071 0.100 48.6 1.77 10.4 0.206 1.95 9.9

6f 90 percent decrease, entire year 18.9 7.17 8.93 0.176 0.074 0.096 16.1 0.61 10.3 0.191 1.65 3.7

2007

1a Base case 18.5 4.60 8.18 0.566 0.071 0.121 85.0 3.51 11.0 0.247 2.50 24.4

6a 25 percent decrease, June–October 18.5 5.38 8.36 0.479 0.080 0.117 68.2 2.80 11.0 0.237 2.32 18.6

6b 50 percent decrease, June–October 18.5 6.19 8.57 0.383 0.086 0.114 50.0 2.06 10.9 0.226 2.13 13.7

6c 90 percent decrease, June–October 18.5 7.47 8.90 0.199 0.090 0.110 15.6 0.77 10.7 0.210 1.76 7.3

6d 25 percent decrease, entire year 18.5 5.45 8.38 0.479 0.080 0.117 68.1 2.79 11.0 0.237 2.32 17.6

6e 50 percent decrease, entire year 18.5 6.35 8.61 0.381 0.087 0.114 49.9 2.06 10.9 0.226 2.13 12.1

6f 90 percent decrease, entire year 18.5 7.77 8.95 0.194 0.091 0.110 15.4 0.77 10.7 0.209 1.76 4.5

2008

1a Base case 18.7 3.17 8.43 0.448 0.044 0.093 67.0 4.61 9.65 0.217 2.32 34.0

6a 25 percent decrease, June–October 18.7 4.03 8.62 0.387 0.056 0.090 53.8 3.55 9.58 0.204 2.13 24.7

6b 50 percent decrease, June–October 18.7 5.06 8.88 0.313 0.065 0.087 39.8 2.51 9.51 0.191 1.92 18.0

6c 90 percent decrease, June–October 18.7 6.86 9.25 0.168 0.073 0.082 13.7 0.77 9.40 0.170 1.55 10.9

6d 25 percent decrease, entire year 18.7 4.10 8.64 0.387 0.056 0.090 53.8 3.54 9.58 0.204 2.13 22.9

6e 50 percent decrease, entire year 18.7 5.24 8.91 0.313 0.066 0.087 39.7 2.48 9.51 0.191 1.92 14.9

6f 90 percent decrease, entire year 18.7 7.21 9.30 0.166 0.074 0.082 13.5 0.74 9.40 0.170 1.54 5.6

2009

1a Base case 18.4 2.85 8.18 0.463 0.067 0.081 43.3 5.08 7.95 0.194 2.20 32.6

6a 25 percent decrease, June–October 18.4 3.70 8.36 0.415 0.084 0.078 35.3 3.88 7.90 0.180 2.01 23.0

6b 50 percent decrease, June–October 18.5 4.79 8.59 0.354 0.099 0.075 26.8 2.71 7.86 0.167 1.81 15.9

6c 90 percent decrease, June–October 18.5 6.77 8.97 0.236 0.112 0.070 10.8 0.82 7.79 0.145 1.45 7.91

6d 25 percent decrease, entire year 18.4 3.80 8.38 0.412 0.085 0.078 35.2 3.87 7.90 0.180 2.01 21.7

6e 50 percent decrease, entire year 18.5 5.00 8.63 0.348 0.101 0.075 26.5 2.69 7.86 0.166 1.80 13.7

6f 90 percent decrease, entire year 18.5 7.20 9.04 0.223 0.114 0.069 10.3 0.78 7.79 0.144 1.44 4.6
52 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon Table A7. Scenario 7 annual volume average results for the Link-Keno reach of the Klamath River, Oregon. [Most scenarios routed the entire river flow through the wetlands; scenarios 7b and 7e treated 250 cubic feet per second (ft3/s). Abbreviations: Seg, model segment; °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter] Scenario Annual in-reach volume average Water temperature (°C) Dissolved oxygen (mg/L) pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L) 2006 1a Base case 11.2 7.91 8.12 0.398 0.161 0.078 41.1 1.72 8.25 0.165 1.84 15.5 7a Seg 28, 50 percent decrease 11.3 8.23 8.18 0.381 0.163 0.077 34.8 1.43 8.17 0.161 1.78 13.5 7b Seg 28, 50 percent decrease, 250 ft3/s 11.2 8.00 8.13 0.394 0.162 0.078 39.7 1.65 8.23 0.164 1.82 14.9 7c Seg 28, 90 percent decrease 11.3 8.47 8.23 0.365 0.164 0.077 29.0 1.18 8.10 0.157 1.72 12.3 7d Seg 54, 50 percent decrease 11.3 8.04 8.14 0.392 0.162 0.078 38.2 1.57 8.21 0.163 1.81 14.6 7e Seg 54, 50 percent decrease, 250 ft3/s 11.2 7.95 8.12 0.396 0.161 0.078 40.4 1.68 8.24 0.164 1.83 15.2 7f Seg 54, 90 percent decrease 11.3 8.14 8.17 0.386 0.162 0.078 35.6 1.45 8.17 0.161 1.78 14.1 2007 1a Base case 11.8 7.60 7.97 0.531 0.204 0.076 36.5 1.84 8.22 0.163 2.03 17.0 7a Seg 28, 50 percent decrease 11.8 7.94 8.04 0.510 0.206 0.075 31.9 1.53 8.13 0.159 1.96 14.3 7b Seg 28, 50 percent decrease, 250 ft3/s 11.8 7.66 7.98 0.526 0.204 0.076 35.1 1.74 8.20 0.162 2.01 16.1 7c Seg 28, 90 percent decrease 11.8 8.22 8.09 0.492 0.208 0.074 27.2 1.26 8.04 0.155 1.89 12.8 7d Seg 54, 50 percent decrease 11.8 7.74 8.00 0.522 0.204 0.076 34.7 1.68 8.17 0.161 1.99 15.9 7e Seg 54, 50 percent decrease, 250 ft3/s 11.8 7.65 7.98 0.529 0.204 0.076 35.9 1.78 8.20 0.163 2.01 16.6 7f Seg 54, 90 percent decrease 11.8 7.86 8.02 0.516 0.205 0.075 32.9 1.55 8.13 0.159 1.96 15.3 2008 1a Base case 11.2 6.75 8.06 0.626 0.199 0.073 32.9 2.54 7.97 0.164 2.17 23.7 7a Seg 28, 50 percent decrease 11.2 7.11 8.11 0.612 0.202 0.072 28.9 2.10 7.87 0.159 2.10 19.3 7b Seg 28, 50 percent decrease, 250 ft3/s 11.2 6.85 8.07 0.622 0.201 0.073 31.8 2.40 7.94 0.162 2.15 22.2 7c Seg 28, 90 percent decrease 11.2 7.43 8.18 0.597 0.204 0.071 25.2 1.75 7.80 0.154 2.03 17.1 7d Seg 54, 50 percent decrease 11.2 6.90 8.08 0.621 0.200 0.073 31.3 2.32 7.91 0.162 2.13 21.9 7e Seg 54, 50 percent decrease, 250 ft3/s 11.2 6.80 8.06 0.624 0.200 0.073 32.4 2.46 7.95 0.163 2.16 23.1 7f Seg 54, 90 percent decrease 11.2 7.04 8.10 0.615 0.201 0.072 29.8 2.15 7.88 0.159 2.10 20.9 2009

1a Base case 11.4 6.95 8.03 0.518 0.159 0.061 22.9 2.67 7.08 0.145 1.93 23.3

7a Seg 28, 50 percent decrease 11.4 7.30 8.09 0.507 0.163 0.060 20.0 2.16 7.01 0.140 1.85 18.3

7b Seg 28, 50 percent decrease, 250 ft3/s 11.4 7.05 8.04 0.515 0.160 0.060 22.1 2.51 7.06 0.144 1.90 21.6

7c Seg 28, 90 percent decrease 11.4 7.64 8.15 0.492 0.165 0.059 17.1 1.77 6.96 0.135 1.78 15.8

7d Seg 54, 50 percent decrease 11.4 7.09 8.05 0.514 0.160 0.060 21.6 2.42 7.04 0.143 1.89 21.3

7e Seg 54, 50 percent decrease, 250 ft3/s 11.4 7.00 8.00 0.517 0.159 0.060 22.5 2.59 7.07 0.144 1.91 22.6

7f Seg 54, 90 percent decrease 11.4 7.24 8.08 0.508 0.160 0.060 20.4 2.23 7.01 0.140 1.85 20.2
Appendix A 53

Table A8. Scenario 7 June through October volume average results for the Link-Keno reach of the Klamath River, Oregon.[Most scenarios treated the entire river flow; scenarios 7b and 7e treated 250 cubic feet per second (ft3/s). Abbreviations: Seg, model segment; °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram 

per liter]

Scenario

June through October in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 18.9 4.42 8.34 0.458 0.060 0.105 84.1 3.12 10.6 0.224 2.27 18.7

7a Seg 28, 50 percent decrease 18.9 5.15 8.49 0.417 0.065 0.103 70.2 2.45 10.4 0.214 2.13 15.0

7b Seg 28, 50 percent decrease, 250 ft3/s 18.9 4.62 8.38 0.448 0.062 0.105 80.8 2.93 10.5 0.221 2.23 17.5

7c Seg 28, 90 percent decrease 18.9 5.71 8.61 0.378 0.067 0.102 57.2 1.89 10.2 0.207 1.99 12.8

7d Seg 54, 50 percent decrease 18.9 4.74 8.41 0.443 0.062 0.104 77.8 2.78 10.4 0.219 2.20 17.0

7e Seg 54, 50 percent decrease, 250 ft3/s 18.9 4.52 8.36 0.454 0.061 0.105 82.5 3.01 10.5 0.223 2.25 18.1

7f Seg 54, 90 percent decrease 18.9 4.99 8.46 0.429 0.062 0.104 72.3 2.51 10.4 0.216 2.14 16.1

2007

1a Base case 18.5 4.60 8.18 0.566 0.071 0.121 85.0 3.51 11.0 0.247 2.50 24.4

7a Seg 28, 50 percent decrease 18.4 5.41 8.34 0.515 0.078 0.118 73.6 2.78 10.8 0.236 2.33 18.5

7b Seg 28, 50 percent decrease, 250 ft3/s 18.4 4.76 8.20 0.553 0.072 0.120 81.4 3.26 11.0 0.244 2.45 22.4

7c Seg 28, 90 percent decrease 18.4 6.07 8.47 0.469 0.082 0.116 62.4 2.17 10.6 0.227 2.18 15.4

7d Seg 54, 50 percent decrease 18.4 4.96 8.25 0.544 0.072 0.120 80.5 3.15 10.9 0.242 2.42 21.9

7e Seg 54, 50 percent decrease, 250 ft3/s 18.5 4.73 8.20 0.560 0.072 0.120 83.5 3.38 11.0 0.245 2.48 23.4

7f Seg 54, 90 percent decrease 18.4 5.26 8.31 0.528 0.073 0.119 76.5 2.85 10.8 0.237 2.35 20.7

2008

1a Base case 18.7 3.17 8.43 0.448 0.044 0.093 67.0 4.61 9.65 0.217 2.32 34.0

7a Seg 28, 50 percent decrease 18.7 3.87 8.56 0.417 0.051 0.091 58.1 3.59 9.42 0.204 2.14 25.3

7b Seg 28, 50 percent decrease, 250 ft3/s 18.7 3.35 8.46 0.439 0.046 0.093 64.5 4.29 9.58 0.213 2.26 31.2

7c Seg 28, 90 percent decrease 18.8 4.61 8.71 0.379 0.055 0.090 49.6 2.79 9.26 0.194 1.98 21.0

7d Seg 54, 50 percent decrease 18.7 3.47 8.48 0.436 0.046 0.092 63.6 4.11 9.53 0.211 2.23 30.5

7e Seg 54, 50 percent decrease, 250 ft3/s 18.7 3.26 8.45 0.444 0.045 0.093 66.0 4.44 9.61 0.215 2.29 32.8

7f Seg 54, 90 percent decrease 18.7 3.79 8.54 0.421 0.047 0.092 60.5 3.73 9.43 0.206 2.16 28.7

2009

1a Base case 18.4 2.85 8.18 0.463 0.067 0.081 43.3 5.08 7.95 0.194 2.20 32.6

7a Seg 28, 50 percent decrease 18.5 3.56 8.30 0.437 0.076 0.079 37.4 3.91 7.78 0.181 2.01 23.0

7b Seg 28, 50 percent decrease, 250 ft3/s 18.5 3.03 8.21 0.456 0.070 0.080 41.6 4.71 7.90 0.190 2.14 29.4

7c Seg 28, 90 percent decrease 18.5 4.33 8.46 0.402 0.083 0.077 31.7 3.01 7.66 0.170 1.85 18.2

7d Seg 54, 50 percent decrease 18.5 3.15 8.23 0.453 0.069 0.080 40.9 4.51 7.86 0.188 2.11 28.7

7e Seg 54, 50 percent decrease, 250 ft3/s 18.5 2.95 8.20 0.460 0.068 0.080 42.5 4.88 7.92 0.192 2.17 31.2

7f Seg 54, 90 percent decrease 18.5 3.50 8.31 0.439 0.070 0.079 38.7 4.08 7.80 0.182 2.03 26.8
54 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon Table A9. Scenario 8 annual volume average results for the Link-Keno reach of the Klamath River, Oregon. 

[Abbreviations: LRDC, Lost River Diversion Channel; KSD, Klamath Straits Drain; °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

Annual in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 11.2 7.91 8.12 0.398 0.161 0.078 41.1 1.72 8.25 0.165 1.84 15.58a Flow to LRDC 11.3 7.97 8.10 0.394 0.164 0.084 38.6 1.64 8.26 0.170 1.83 14.78b Flow to KSD 11.2 7.95 8.08 0.400 0.163 0.084 36.7 1.61 8.42 0.171 1.85 14.78c Flow to LRDC and KSD 11.3 7.96 8.09 0.397 0.164 0.084 37.5 1.62 8.34 0.170 1.84 14.7

2007

1a Base case 11.8 7.60 7.97 0.531 0.204 0.076 36.5 1.84 8.22 0.163 2.03 17.08a Flow to LRDC 11.9 7.56 7.96 0.523 0.206 0.081 33.9 1.73 8.13 0.166 1.99 16.18b Flow to KSD 11.8 7.64 7.94 0.546 0.207 0.083 31.3 1.69 8.44 0.171 2.05 16.1

8c Flow to LRDC and KSD 11.8 7.60 7.94 0.535 0.207 0.082 32.5 1.71 8.30 0.169 2.03 16.1

2008

1a Base case 11.2 6.75 8.06 0.626 0.199 0.073 32.9 2.54 7.97 0.164 2.17 23.7

8a Flow to LRDC 11.3 6.77 8.00 0.628 0.202 0.077 31.1 2.40 7.98 0.167 2.16 22.5

8b Flow to KSD 11.2 6.82 8.00 0.638 0.204 0.079 29.1 2.33 8.19 0.171 2.19 22.3

8c Flow to LRDC and KSD 11.2 6.79 8.01 0.633 0.203 0.078 30.1 2.37 8.08 0.169 2.18 22.4

2009

1a Base case 11.4 6.95 8.03 0.518 0.159 0.061 22.9 2.67 7.08 0.145 1.93 23.3

8a Flow to LRDC 11.4 6.96 8.02 0.520 0.159 0.067 22.2 2.53 7.08 0.151 1.91 22.1

8b Flow to KSD 11.3 7.00 7.99 0.524 0.159 0.066 20.9 2.46 7.33 0.151 1.94 22.2

8c Flow to LRDC and KSD 11.4 6.98 8.00 0.522 0.159 0.066 21.5 2.50 7.21 0.151 1.93 22.2
Appendix A 55

Table A10. Scenario 8 June through October volume average results for the Link-Keno reach of the Klamath River, Oregon. [Abbreviations: LRDC, Lost River Diversion Channel; KSD, Klamath Straits Drain; °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

Annual in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 18.9 4.42 8.34 0.458 0.060 0.105 84.1 3.12 10.6 0.224 2.27 18.78a Flow to LRDC 18.9 4.55 8.29 0.453 0.069 0.121 77.3 2.89 10.6 0.238 2.25 17.28b Flow to KSD 18.9 4.44 8.23 0.469 0.065 0.120 72.9 2.83 11.0 0.240 2.31 17.38c Flow to LRDC and KSD 18.9 4.49 8.26 0.460 0.067 0.119 74.8 2.86 10.8 0.238 2.28 17.3

2007

1a Base case 18.5 4.60 8.18 0.566 0.071 0.121 85.0 3.51 11.0 0.247 2.50 24.48a Flow to LRDC 18.4 4.52 8.14 0.548 0.078 0.132 77.4 3.20 10.8 0.253 2.42 22.6

8b Flow to KSD 18.5 4.62 8.08 0.609 0.078 0.140 71.5 3.13 11.6 0.268 2.58 22.5

8c Flow to LRDC and KSD 18.4 4.58 8.11 0.579 0.079 0.136 74.3 3.17 11.2 0.261 2.50 22.5

2008

1a Base case 18.7 3.17 8.43 0.448 0.044 0.093 67.0 4.61 9.65 0.217 2.32 34.0

8a Flow to LRDC 18.7 3.18 8.36 0.457 0.051 0.104 62.0 4.24 9.66 0.224 2.29 31.7

8b Flow to KSD 18.7 3.27 8.28 0.483 0.055 0.110 57.4 4.08 10.2 0.234 2.37 31.1

8c Flow to LRDC and KSD 18.7 3.21 8.32 0.470 0.053 0.106 59.7 4.17 9.94 0.229 2.33 31.6

2009

1a Base case 18.4 2.85 8.18 0.463 0.067 0.081 43.3 5.08 7.95 0.194 2.20 32.6

8a Flow to LRDC 18.5 2.86 8.15 0.470 0.068 0.097 41.1 4.69 7.96 0.207 2.16 30.6

8b Flow to KSD 18.5 2.92 8.08 0.479 0.067 0.094 38.2 4.54 8.61 0.209 2.23 30.4

8c Flow to LRDC and KSD 18.5 2.88 8.10 0.475 0.067 0.095 39.6 4.63 8.29 0.207 2.20 30.6
56 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon Table A11. Scenario 9 dissolved oxygen supplementation annual volume average results for the Link-Keno reach of the Klamath River, Oregon.

[Abbreviations: DO, dissolved oxygen; °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

Annual in-reach volume average

Water 

temperature

°C

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 11.2 7.91 8.12 0.398 0.161 0.078 41.1 1.72 8.25 0.165 1.84 15.5

9a DO saturation, segment 7 (Railroad Bridge) 11.2 8.35 8.12 0.394 0.164 0.077 41.1 1.72 8.23 0.164 1.84 14.99b DO saturation, segment 21 (Highway 97) 11.2 8.51 8.13 0.392 0.165 0.078 40.7 1.71 8.23 0.164 1.83 14.8

9c DO saturation, segment 38 (Miller Island) 11.2 8.33 8.11 0.397 0.163 0.078 41.0 1.71 8.24 0.165 1.84 15.2

9d DO supersaturation, segment 7 (Railroad Bridge) 11.2 9.08 8.10 0.399 0.166 0.078 41.0 1.71 8.24 0.165 1.84 15.0

9e DO supersaturation, segment 21 (Highway 97) 11.2 9.21 8.10 0.399 0.166 0.078 41.0 1.71 8.24 0.165 1.84 15.0

9f DO supersaturation, segment 38 (Miller Island) 11.3 9.23 8.13 0.394 0.167 0.078 40.4 1.71 8.23 0.164 1.84 14.6

2007

1a Base case 11.8 7.60 7.97 0.531 0.204 0.076 36.5 1.84 8.22 0.163 2.03 17.0

9a DO saturation, segment 7 (Railroad Bridge) 11.8 7.74 7.95 0.532 0.205 0.075 37.1 1.85 8.24 0.162 2.03 16.8

9b DO saturation, segment 21 (Highway 97) 11.8 7.88 7.95 0.535 0.207 0.076 36.8 1.84 8.23 0.164 2.03 16.4

9c DO saturation, segment 38 (Miller Island) 11.8 7.88 7.95 0.535 0.205 0.076 36.6 1.83 8.23 0.164 2.03 16.2

9d DO supersaturation, segment 7 (Railroad Bridge) 11.8 8.65 7.94 0.536 0.210 0.077 36.6 1.83 8.23 0.164 2.04 15.8

9e DO supersaturation, segment 21 (Highway 97) 11.8 8.79 7.94 0.537 0.210 0.077 36.6 1.83 8.23 0.164 2.04 15.6

9f DO supersaturation, segment 38 (Miller Island) 11.8 8.68 7.94 0.536 0.207 0.077 36.6 1.83 8.23 0.164 2.03 15.7

2008

1a Base case 11.2 6.75 8.06 0.626 0.199 0.073 32.9 2.54 7.97 0.164 2.17 23.7

9a DO saturation, segment 7 (Railroad Bridge) 11.2 7.03 8.04 0.628 0.203 0.072 33.3 2.54 7.96 0.164 2.18 22.4

9b DO saturation, segment 21 (Highway 97) 11.2 7.21 8.03 0.631 0.204 0.073 33.0 2.52 7.96 0.164 2.18 21.6

9c DO saturation, segment 38 (Miller Island) 11.2 7.22 8.04 0.629 0.202 0.073 32.9 2.52 7.96 0.164 2.18 21.8

9d DO supersaturation, segment 7 (Railroad Bridge) 11.2 7.75 8.03 0.633 0.206 0.073 32.8 2.51 7.96 0.164 2.18 21.0

9e DO supersaturation, segment 21 (Highway 97) 11.2 7.89 8.02 0.634 0.207 0.073 32.8 2.50 7.96 0.164 2.18 20.5

9f DO supersaturation, segment 38 (Miller Island) 11.2 7.81 8.03 0.631 0.203 0.073 32.8 2.51 7.96 0.164 2.18 21.0

2009

1a Base case 11.4 6.95 8.03 0.518 0.159 0.061 22.9 2.67 7.08 0.145 1.93 23.3

9a DO saturation, segment 7 (Railroad Bridge) 11.3 7.27 8.00 0.522 0.164 0.060 23.1 2.67 7.07 0.144 1.94 21.9

9b DO saturation, segment 21 (Highway 97) 11.3 7.44 7.99 0.524 0.166 0.061 23.0 2.65 7.07 0.146 1.94 21.0

9c DO saturation, segment 38 (Miller Island) 11.4 7.45 8.00 0.522 0.163 0.061 22.9 2.65 7.07 0.145 1.93 21.0

9d DO supersaturation, segment 7 (Railroad Bridge) 11.3 7.91 7.99 0.526 0.169 0.061 22.9 2.64 7.07 0.146 1.94 20.5

9e DO supersaturation, segment 21 (Highway 97) 11.4 8.08 7.98 0.527 0.170 0.061 22.9 2.63 7.07 0.146 1.94 19.9

9f DO supersaturation, segment 38 (Miller Island) 11.4 8.03 8.03 0.524 0.164 0.061 22.9 2.64 7.07 0.145 1.93 20.3
Appendix A 57

Table A12. Scenario 9 dissolved oxygen supplementation June through October volume average results for the Link-Keno reach of the Klamath River, Oregon.[Abbreviations: DO, dissolved oxygen; °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

June through October in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 18.9 4.42 8.34 0.458 0.060 0.105 84.1 3.12 10.6 0.224 2.27 18.7

9a DO saturation, segment 7 (Railroad Bridge) 19.0 5.43 8.36 0.454 0.068 0.103 84.9 3.14 10.6 0.222 2.28 17.3

9b DO saturation, segment 21 (Highway 97) 19.0 5.84 8.38 0.449 0.070 0.104 83.8 3.11 10.6 0.223 2.27 17.2

9c DO saturation, segment 38 (Miller Island) 18.9 5.42 8.32 0.461 0.065 0.105 84.0 3.10 10.6 0.224 2.28 17.9

9d DO supersaturation, segment 7 (Railroad Bridge) 18.8 7.33 8.30 0.464 0.073 0.106 84.2 3.10 10.6 0.224 2.29 17.6

9e DO supersaturation, segment 21 (Highway 97) 18.9 7.67 8.30 0.464 0.072 0.106 84.2 3.10 10.5 0.224 2.29 17.5

9f DO supersaturation, segment 38 (Miller Island) 18.9 7.45 8.29 0.462 0.069 0.106 84.1 3.10 10.6 0.224 2.28 17.5

2007

1a Base case 18.5 4.60 8.18 0.566 0.071 0.121 85.0 3.51 11.0 0.247 2.50 24.4

9a DO saturation, segment 7 (Railroad Bridge) 18.4 4.99 8.13 0.568 0.074 0.117 85.9 3.51 11.1 0.243 2.51 23.79b DO saturation, segment 21 (Highway 97) 18.4 5.35 8.12 0.575 0.078 0.122 85.2 3.49 11.0 0.248 2.52 22.9

9c DO saturation, segment 38 (Miller Island) 18.4 5.35 8.12 0.575 0.075 0.122 84.6 3.48 11.0 0.248 2.51 22.59d DO supersaturation, segment 7 (Railroad Bridge) 18.4 7.26 8.10 0.579 0.087 0.122 84.7 3.46 11.0 0.248 2.53 21.59e DO supersaturation, segment 21 (Highway 97) 18.4 7.62 8.10 0.580 0.086 0.122 84.7 3.46 11.0 0.248 2.53 20.9

9f DO supersaturation, segment 38 (Miller Island) 18.4 7.38 8.11 0.577 0.080 0.122 84.6 3.46 11.0 0.248 2.52 21.3

2008

1a Base case 18.7 3.17 8.43 0.448 0.044 0.093 67.0 4.61 9.65 0.217 2.32 34.09a DO saturation, segment 7 (Railroad Bridge) 18.7 3.80 8.38 0.456 0.052 0.092 68.0 4.61 9.63 0.216 2.34 31.3

9b DO saturation, segment 21 (Highway 97) 18.7 4.22 8.37 0.463 0.056 0.094 67.3 4.57 9.63 0.218 2.34 29.8

9c DO saturation, segment 38 (Miller Island) 18.7 4.27 8.38 0.458 0.050 0.094 66.9 4.57 9.63 0.217 2.33 30.0

9d DO supersaturation, segment 7 (Railroad Bridge) 18.7 5.57 8.34 0.469 0.062 0.095 66.8 4.53 9.62 0.218 2.35 28.2

9e DO supersaturation, segment 21 (Highway 97) 18.7 5.93 8.33 0.472 0.062 0.095 66.8 4.52 9.62 0.218 2.35 27.1

9f DO supersaturation, segment 38 (Miller Island) 18.7 5.74 8.36 0.464 0.054 0.094 66.8 4.55 9.63 0.217 2.34 28.3

2009

1a Base case 18.4 2.85 8.18 0.463 0.067 0.081 43.3 5.08 7.95 0.194 2.20 32.6

9a DO saturation, segment 7 (Railroad Bridge) 18.4 3.59 8.11 0.474 0.079 0.079 43.8 5.07 7.93 0.192 2.22 29.7

9b DO saturation, segment 21 (Highway 97) 18.4 3.98 8.08 0.481 0.085 0.082 43.4 5.02 7.93 0.195 2.23 28.0

9c DO saturation, segment 38 (Miller Island) 18.5 4.02 8.11 0.476 0.077 0.081 43.2 5.03 7.94 0.194 2.22 28.0

9d DO supersaturation, segment 7 (Railroad Bridge) 18.4 5.15 8.06 0.485 0.094 0.082 43.2 4.99 7.93 0.194 2.24 27.0

9e DO supersaturation, segment 21 (Highway 97) 18.4 5.58 8.05 0.488 0.096 0.082 43.1 4.97 7.92 0.194 2.24 25.6

9f DO supersaturation, segment 38 (Miller Island) 18.5 5.48 8.09 0.481 0.081 0.082 43.2 5.00 7.93 0.194 2.22 26.3
58 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon Table A13. Scenario 9 annual volume average results for the Link-Keno reach of the Klamath River, Oregon.

[Abbreviations: DO, dissolved oxygen; °C, degrees Celsius; m, meter; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

Annual in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 11.2 7.91 8.12 0.398 0.161 0.078 41.1 1.72 8.25 0.165 1.84 15.5

9g Shade, 10 m trees 11.1 7.84 8.10 0.396 0.161 0.079 40.3 1.69 8.24 0.165 1.83 15.3

9g Shade, 20 m trees 11.0 7.82 8.09 0.396 0.162 0.079 40.0 1.68 8.24 0.165 1.83 15.3

2007

1a Base case 11.8 7.60 7.97 0.531 0.204 0.076 36.5 1.84 8.22 0.163 2.03 17.0

9g Shade, 10 m trees 11.7 7.43 7.93 0.527 0.203 0.076 35.7 1.79 8.21 0.163 2.01 16.7

9g Shade, 20 m trees 11.5 7.37 7.91 0.527 0.203 0.077 35.5 1.78 8.21 0.163 2.01 16.8

2008

1a Base case 11.2 6.75 8.06 0.626 0.199 0.073 32.9 2.54 7.97 0.164 2.17 23.7

9g Shade, 10 m trees 11.1 6.67 7.97 0.622 0.199 0.073 32.3 2.51 7.96 0.164 2.16 23.4

9g Shade, 20 m trees 10.9 6.64 8.03 0.622 0.199 0.073 32.1 2.50 7.96 0.164 2.16 23.3

2009

1a Base case 11.4 6.95 8.03 0.518 0.159 0.061 22.9 2.67 7.08 0.145 1.93 23.3

9g Shade, 10 m trees 11.2 6.90 8.01 0.516 0.159 0.061 22.5 2.65 7.07 0.145 1.92 23.2

9g Shade, 20 m trees 11.1 6.88 8.00 0.516 0.159 0.061 22.3 2.64 7.07 0.145 1.92 23.0
Appendix A 59

Table A14. Scenario 9 June through October volume average results for the Link-Keno reach of the Klamath River, Oregon.[Abbreviations: DO, dissolved oxygen; °C, degrees Celsius; m, meter; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

June through October in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2006

1a Base case 18.9 4.42 8.34 0.458 0.060 0.105 84.1 3.12 10.6 0.224 2.27 18.7

9g Shade, 10 m trees 18.7 4.30 8.30 0.453 0.060 0.106 82.0 3.04 10.5 0.224 2.26 18.1

9g Shade, 20 m trees 18.5 4.27 8.29 0.452 0.061 0.106 81.3 3.02 10.5 0.224 2.25 17.9

2007

1a Base case 18.5 4.60 8.18 0.566 0.071 0.121 85.0 3.51 11.0 0.247 2.50 24.4

9g Shade, 10 m trees 18.2 4.30 8.11 0.555 0.069 0.121 82.8 3.39 11.0 0.247 2.47 23.6

9g Shade, 20 m trees 18.0 4.16 8.09 0.555 0.067 0.122 82.0 3.35 11.0 0.247 2.46 23.6

2008

1a Base case 18.7 3.17 8.43 0.448 0.044 0.093 67.0 4.61 9.65 0.217 2.32 34.0

9g Shade, 10 m trees 18.5 3.06 8.36 0.443 0.044 0.094 65.6 4.55 9.63 0.217 2.31 33.5

9g Shade, 20 m trees 18.3 3.03 8.39 0.442 0.044 0.094 65.1 4.52 9.62 0.217 2.30 33.1

2009

1a Base case 18.4 2.85 8.18 0.463 0.067 0.081 43.3 5.08 7.95 0.194 2.20 32.6

9g Shade, 10 m trees 18.3 2.75 8.15 0.459 0.067 0.081 42.4 5.02 7.93 0.193 2.19 32.1

9g Shade, 20 m trees 18.1 2.72 8.14 0.459 0.067 0.081 42.0 5.00 7.92 0.193 2.18 31.7
60 Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon Table A15. Scenario 10 annual volume-average results for the Link-Keno reach of the Klamath River, Oregon.

[Abbreviations: °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

Annual in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2007

1a Base case 11.8 7.60 7.97 0.531 0.204 0.076 36.5 1.84 8.22 0.163 2.03 17.0

10a Minimum future temperature increase 12.4 7.54 7.96 0.531 0.204 0.076 36.4 1.83 8.21 0.163 2.02 16.6

10b Median future temperature increase 13.2 7.45 7.96 0.531 0.203 0.075 36.2 1.83 8.19 0.163 2.02 16.0

10c Maximum future temperature increase 14.2 7.35 7.95 0.531 0.202 0.075 36.1 1.82 8.18 0.162 2.02 15.6

Table A16. Scenario 10 June through October volume average concentrations for the Link-Keno reach of the Klamath River, Oregon.[Abbreviations: °C, degrees Celsius; mg/L, milligram per liter; μg/L, microgram per liter]

Scenario

June through October in-reach volume average

Water 

temperature

(°C)

Dissolved 

oxygen

(mg/L)

pH Ammonia (mg/L) Nitrate (mg/L) Ortho- phosphorus (mg/L) Chlorophyll a (μg/L) Particulate organic carbon (mg/L) Dissolved organic carbon (mg/L) Total phosphorus (mg/L) Total nitrogen (mg/L) Sediment (1st-order) (mg/L)

2007

1a Base case 18.5 4.60 8.18 0.566 0.071 0.121 85.0 3.51 11.0 0.247 2.50 24.4

10a Minimum future temperature increase 19.1 4.49 8.16 0.567 0.070 0.120 85.0 3.50 11.0 0.247 2.50 24.1

10b Median future temperature increase 19.9 4.35 8.14 0.570 0.069 0.120 85.0 3.49 11.0 0.246 2.50 23.8

10c Maximum future temperature increase 20.7 4.26 8.14 0.571 0.068 0.120 85.2 3.50 11.0 0.246 2.50 23.8
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 Publishing Network, Tacoma Publishing Service Center

For more information concerning the research in this report, contact the

Director, Oregon Water Science Center

U.S. Geological Survey

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Portland, Oregon 97201

http://or.water.usgs.gov
Sullivan and others— Modeling the Water-Quality Effects of Changes to the Klamath River Upstream of Keno Dam, Oregon—Scientific Investigations Report 2013–5135