U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2018–5075

Prepared in cooperation with the Bureau of Reclamation

Nutrient Loads in the Lost River and 

Klamath River Basins, South-Central 

Oregon and Northern California, 

March 2012–March 2015

Nutrient Loads in the Lost River and 

Klamath River Basins, South-Central 

Oregon and Northern California, 

March 2012–March 2015

By Liam N. Schenk, Marc A. Stewart, and Sara L. Caldwell Eldridge

Prepared in cooperation with the Bureau of Reclamation

Scientific Investigations Report 2018–5075

U.S. Department of the Interior

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

RYAN K. ZINKE, Secretary

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2018

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Suggested citation:

Schenk, L.N., Stewart, M.A., and Eldridge, S.L.C., 2018, Nutrient loads in the Lost River and Klamath River 

Basins, south-central Oregon and northern California, March 2012–March 2015: U.S. Geological Survey Scientific 

Investigations Report 2018–5075, 55 p., https://doi.org/10.3133/sir20185075.

ISSN 2328-0328 (online)
iii

Contents

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

Introduction.....................................................................................................................................................2

Background............................................................................................................................................2

Purpose and Scope ..............................................................................................................................3

Description of Study Area ..................................................................................................................3

Methods...........................................................................................................................................................5

Sampling Sites.......................................................................................................................................5

Collection of Water-Quality Samples.................................................................................................7

Streamflow Data ...................................................................................................................................9

Load Estimation.....................................................................................................................................9

LOADEST Models.......................................................................................................................10

Instantaneous and Daily Load Averaging..............................................................................11

Quality Assurance .......................................................................................................................................12

Bureau of Reclamation Quality Assurance ....................................................................................12

U.S. Geological Survey Quality Assurance ....................................................................................12

Quality Assurance Results ................................................................................................................13

Bureau of Reclamation Quality Assurance Results.............................................................13

U.S. Geological Survey Quality Assurance Results .............................................................13

Results ...........................................................................................................................................................14

Streamflow...........................................................................................................................................14

Water-Quality Concentrations..........................................................................................................14

Total Nutrients ............................................................................................................................16

Dissolved Nutrients ...................................................................................................................18

Five-Day Biochemical Oxygen Demand (BOD5), 5-Day Carbonaceous Biochemical 

Oxygen Demand (CBOD5), and Chlorophyll-a..........................................................23

Dissolved Organic Carbon, Total Particulate Carbon, and Total Particulate 

Nitrogen ........................................................................................................................23

Load Estimates ....................................................................................................................................28

Klamath River at Keno (Site KRK) LOADEST Model Results...............................................29

Fremont Bridge (site FMT) LOADEST Model Results...........................................................32

Instantaneous and Daily Load Averaging Results................................................................34

Upper Lost River Basin Sites ...................................................................................................37

Tule Lake Sites............................................................................................................................40

Klamath Drainage District Sites and Site LRDC....................................................................40

Discussion.....................................................................................................................................................44

Nutrient, 5-Day Biochemical Oxygen Demand, and 5-Day Carbonaceous Biochemical 

Oxygen Demand Loading within the Klamath Project.....................................................44

Nutrient Budget for Klamath River from Link River Dam to Keno Dam......................................45

Organic Carbon and Nitrogen...........................................................................................................51

Nutrient Loads and Total Maximum Daily Loads ...........................................................................51

Suggestions for Future Studies ........................................................................................................51
iv

Acknowledgments.......................................................................................................................................53

References Cited..........................................................................................................................................53

Appendix 1. Loadest Model Summaries for Rejected Models.............................................................55

Contents—Continued

Figures

1. Map showing sample and data collection sites, Klamath River and Lost River

Basins, south-central Oregon and northern California, March 2012–March 2015............4

2. Boxplot showing mean annual streamflow at Williamson River near Chiloquin 

(U.S. Geological Survey streamgage 11502500), Upper Klamath Basin, southcentral Oregon, water years (WYs) 1976–2015, and reference lines for 

WYs 2012–15..................................................................................................................................5

3. Schematic representation of the Link River (connecting Upper Klamath Lake to

Lake Ewauna) showing flows used to estimate instantaneous streamflow at site

FMT, Upper Klamath Basin, south-central Oregon ...............................................................10

4. Graphs showing mean streamflow at study sites during irrigation and nonirrigation seasons, Klamath River and Lost River Basins, Oregon and California, 

March 2012–March 2015 ...........................................................................................................15

5. Boxplots showing nutrient concentrations at end member sites, south-central

Oregon, March 2012–March 2015............................................................................................19

6. Boxplots showing nutrient concentrations at upper Lost River Basin sites,

south-central Oregon, March 2012–March 2015...................................................................20

7. Boxplots showing nutrient concentrations at Tule Lake sites, northern California,

March 2012–March 2015 ...........................................................................................................21

8. Boxplots showing nutrient concentrations at Klamath Drainage District sites,

south-central Oregon, March 2012–March 2015...................................................................22

9. Boxplots showing 5-day biochemical oxygen demand, 5-day carbonaceous

biochemical oxygen demand, and chlorophyll-a sample results at end member

sites, south-central Oregon, March 2012–March 2015 ........................................................24

10. Boxplots showing 5-day biochemical oxygen demand, 5-day carbonaceous

biochemical oxygen demand, and chlorophyll-a sample results at upper Lost River

Basin sites, south-central Oregon, March 2012–March 2015.............................................25

11. Boxplots showing 5-day biochemical oxygen demand, 5-day carbonaceous

biochemical oxygen demand, and chlorophyll-a sample results at Tule Lake sites,

northern California, March 2012–March 2015 .......................................................................26

12. Boxplots showing 5-day biochemical oxygen demand, 5-day carbonaceous

biochemical oxygen demand, and chlorophyll-a sample results at Klamath

Drainage District sites, south-central Oregon, March 2012–March 2015.........................27

13. Graphs showing seasonal peak concentrations of total phosphorus at site FMT,

total nitrogen at site FMT, total phosphorus at site KRK, and total nitrogen at site

KRK, south-central Oregon, March 2012–March 2015 .........................................................29
v

14. Time series of computed daily loads, associated 95-percent prediction intervals, 

and observed instantaneous loads of total phosphorus, and total nitrogen at 

site KRK, south-central Oregon, March 2012–March 2015..................................................31

15. Time series of computed daily loads, associated 95-percent prediction intervals,

and observed instantaneous loads of 5-day biochemical oxygen demand, and

5-day carbonaceous biochemical oxygen demand at site KRK, south-central

Oregon, March 2012–March 2015............................................................................................33

16. Graphs showing percent difference between modeled (LOADEST) and measured

loads for total phosphorus, total nitrogen, 5-day biochemical oxygen demand, and

5-day carbonaceous biochemical oxygen demand at site KRK, south-central

Oregon, March 2012–March 2015............................................................................................34

17. Time series of computed daily loads, associated 95-percent prediction intervals,

and observed instantaneous loads of total phosphorus, and total nitrogen at site

FMT, south-central Oregon, March 2012–March 2015 .........................................................35

18. Time series of computed daily loads, associated 95-percent prediction intervals,

and observed instantaneous loads of 5-day biochemical oxygen demand, and

5-day carbonaceous biochemical oxygen demand at site FMT, south-central

Oregon, March 2012–March 2015............................................................................................36

19. Graphs showing percent difference between modeled (LOADEST) and measured

loads for total phosphorus, total nitrogen, 5-day biochemical oxygen demand, and

5-day carbonaceous biochemical oxygen demand at site FMT, March 2012–March

2015, south-central Oregon.......................................................................................................37

20. Graphs showing total phosphorus, total nitrogen, 5-day biochemical oxygen

demand, and 5-day carbonaceous biochemical oxygen demand loads along the

Klamath River flowpath from sites FMT to KRK, south-central Oregon, March

2012–13 (study year 1)................................................................................................................46

21. Graphs showing total phosphorus, total nitrogen, 5-day biochemical oxygen

demand, and 5-day carbonaceous biochemical oxygen demand loads along the

Klamath River flowpath from sites FMT to KRK, south-central Oregon, March

2013–14 (study year 2)................................................................................................................47

22. Graphs showing total phosphorus, total nitrogen, 5-day biochemical oxygen

demand, and 5-day carbonaceous biochemical oxygen demand loads along the

Klamath River flowpath from sites FMT to KRK, south-central Oregon, March

2014–15 (study year 3)................................................................................................................48

23. Graphs showing average daily loads of total phosphorus, total nitrogen, and 5-day

biochemical oxygen demand and Total Maximum Daily Load (TMDL) load 

allocations at site KSD97, south-central Oregon ..................................................................52

24. Graphs showing average daily loads of total phosphorus, total nitrogen, and 5-day

biochemical oxygen demand, and Total Maximum Daily Load (TMDL) load 

allocations at site LRDC, south-central Oregon ....................................................................52

Figures—Continued
vi

Tables

1. Water-quality sampling sites, Lost River Basin, south-central Oregon and 

northern California, March 2012–March 2015 .........................................................................6

2. Study years and responsible sampling agencies....................................................................7

3. Laboratory analysis methods and method reporting limits for this study, 

March 2012–March 2015 .............................................................................................................8

4. Quality-control data for Bureau of Reclamation water-quality samples, Klamath

River and Lost River drainages, south-central Oregon and northern California..............13

5. Quality-control data for U.S. Geological Survey water-quality samples, Klamath

River and Lost River drainages, south-central Oregon and northern California..............13

6. Summary statistics of total and dissolved nutrient sample results, Klamath River

and Lost River Basins, south-central Oregon and northern California, March

2012–March 2015 ........................................................................................................................17

7. Summary statistics of 5-day biochemical oxygen demand, 5-day carbonaceous

biochemical oxygen demand, and chlorophyll-a sample results, Klamath River and

Lost River Basins, south-central Oregon and northern California, March 2012–

March 2015 ..................................................................................................................................18

8. Sample concentration results from all sites ..........................................................................18

9. Summary statistics of dissolved organic carbon, total particulate carbon, and 

total particulate nitrogen sample results, Klamath River and Lost River Basins,

south-central Oregon and northern California, March 2012–March 2015 ........................28

10. Model statistics for LOADEST results at Klamath River at sites KRK and FMT,

south-central Oregon.................................................................................................................30

11. Average modeled (LOADEST) mean daily loads of total phosphorus, total nitrogen,

5-day biochemical oxygen demand, and 5-day carbonaceous biochemical oxygen

demand at sites FMT and KRK during irrigation and non-irrigation seasons,

south-central Oregon, March 2012–March 2015...................................................................38

12. Averaged instantaneous loads of total phosphorus, total nitrogen, 5-day

biochemical oxygen demand, and 5-day carbonaceous biochemical oxygen

demand, during irrigation and non-irrigation seasons, at upper Lost River 

Basin sites LRBM, MCRV, and LRBH, Lost River and Klamath River Basins, 

south-central Oregon, March 2012–March 2015...................................................................39

13. Averaged instantaneous loads at the Tule Lake sites of total phosphorus, total

nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous 

biochemical oxygen demand during irrigation and non-irrigation seasons at sites 

LREW and PDD, Lost River and Klamath River Basins, northern California, 

March 2012–March 2015 ...........................................................................................................41

14. Averaged instantaneous loads of total phosphorus, total nitrogen, 5-day

biochemical oxygen demand, and 5-day carbonaceous biochemical oxygen

demand during irrigation and non-irrigation seasons at Klamath Drainage District

sites (KSDH, ADC97, NC, LRDC, and KSD97) and site LRDC, Lost River and Klamath

River Basins, south-central Oregon, March 2012–March 2015 ..........................................42

15. Average of modeled mean daily loads (using LOADEST) of total phosphorus, 

total nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous 

biochemical oxygen demand during irrigation seasons to account for A Canal 

diversions at sites KRK and FMT, including a 38-percent reduction in loads at 

site FMT, south-central Oregon, March 2012–March 2015..................................................44
vii

16. Nutrient load and streamflow balance using average of modeled mean daily loads

(using LOADEST) total phosphorus, total nitrogen, 5-day biochemical oxygen

demand, and 5-day carbonaceous biochemical oxygen demand at sites KRK and

FMT, and average of daily loads at sites LRDC, NC, ADC97, and KSD97,

south-central Oregon, March 2012–March 2015...................................................................49

Tables—Continued

Conversion Factors

U.S. customary units to International System of Units

Multiply By To obtain

Flow rate

inch per second (in/s) 25.4 millimeter per second (mm/s)

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

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

International System of Units to U.S. customary units

Multiply By To obtain

Length

micron (μm) 0.00003937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

kilometer (km) 0.6214 mile (mi)

Area

square kilometer (km2) 0.3861 square mile (mi2)

Volume

milliliter (mL) 0.03382 ounce, fluid (fl. oz)

liter (L) 33.82 ounce, fluid (fl. oz)

Flow rate

meter per second (m/s) 3.281 foot per second (ft/s)

cubic meter per second (m3/s) 70.07 cubic foot per second (ft3/s) 

Mass

milligram (mg) 0.00003527 ounce, avoirdupois (oz)

kilogram per day (kg/d) 2.205 pound avoirdupois per day (lb/d)

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

°F = (1.8 × °C) + 32.

Datum

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

Supplemental Information

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

or micrograms per liter (μg/L).

Abbreviations

AFA Aphanizomenon flos-aquae

AIC Akaike Information Criterion

AMLE adjusted maximum likelihood estimation

BO Biological Opinion

BOD5 5-day biochemical oxygen demand

Bp load bias in percent

CBOD5 5-day carbonaceous biochemical oxygen demand

DI deionized

DOC dissolved organic carbon

EWI equal-width-increment

HDPE high-density polyethylene

MLE maximum likelihood estimation

MRL minimum reporting level

N Nitrogen

NH3 dissolved ammonia as N

NO3+NO2 dissolved nitrate plus nitrite as N

NWQL National Water Quality Laboratory

ODEQ Oregon Department of Environmental Quality

ortho-P dissolved orthophosphate as P

P Phosphorus

PPCC probability plot correlation coefficient

QA quality assurance

R2 coefficient of determination

Reclamation Bureau of Reclamation

RPD relative percent difference

SPCC Schwarz Posterior Probability Criterion

SRWQL Sprague River Water Quality Laboratory

TKN Total Kjelhahl Nitrogen

TMDL Total Maximum Daily Load

TN total nitrogen

TP total phosphorus

TPC total particulate carbon

TPN total particulate nitrogen

USGS U.S. Geological Survey

WY water year
Nutrient Loads in the Lost River and Klamath River 

Basins, South-Central Oregon and Northern California, 

March 2012–March 2015

By Liam N. Schenk, Marc A. Stewart, and Sara L. Caldwell Eldridge

Significant Findings

The U.S. Geological Survey and Bureau of Reclamation 

collected water-quality data from March 2012 to March 2015 

at locations in the Lost River and Klamath River Basins, 

Oregon, in an effort to characterize water quality and compute 

a nutrient budget for the Bureau of Reclamation Klamath 

Reclamation Project. The study described in this report 

resulted in the following significant findings:

• Total phosphorus (TP), total nitrogen (TN), 5-day 

biochemical oxygen demand (BOD5), and 5-day 

carbonaceous biochemical oxygen demand (CBOD5) 

loads, calculated using the U.S. Geological Survey 

LOADEST software package at the upper and lower 

boundaries of the Klamath Reclamation Project, 

indicated higher loads at the upper boundary on the 

southern end of Upper Klamath Lake upstream of the 

Bureau of Reclamation A Canal diversion compared to 

the lower boundary on the Klamath River downstream 

of Keno Dam. Accounting for the diversion of loads 

down A Canal, BOD5 and CBOD5 loads decreased 

between these two sites during irrigation season, 

indicating that the Klamath Reclamation Project is 

not a large source of oxygen-demanding material and 

that much of the oxygen demand at study site FMT, 

the northern boundary of the study area, has been 

expressed by the time the same water passes through 

site KRK, the southern boundary of the study area.

• An evaluation of the nutrient balance along the 

Klamath River flowpath from sites FMT to KRK 

indicated that, during irrigation season in the 3 years 

of the study period (March 2012–March 2015), more 

loads of TP, TN, BOD5, and CBOD5 were being 

diverted from the Klamath River than were being 

added to the Klamath River from the combination 

of Klamath Straits Drain, regulated point sources 

along the Klamath River, and internal loading from 

the bottom sediments in the river. By contrast, during 

non-irrigation seasons, more loads were added to the 

Klamath River than were diverted through Ady and 

North Canals, and this difference primarily was due 

to additional loads to the river from the Lost River 

Diversion Channel.

• At the Lost River Diversion Channel, BOD5 loads were 

higher during irrigation season than non-irrigation 

season in all three study years owing to the high 

concentrations of oxygen-demanding cyanobacterial 

biomass from the seasonal blooms of Aphanizomenon 

flos-aquae in the Klamath River and Upper Klamath 

Lake. The difference between the two seasons was 

particularly large in years 2 and 3, when the low flows 

of these two drought years resulted in smaller nonirrigation period loads than in year 1. CBOD5 loads 

also were higher during irrigation season in years 2 and 

3 than during non-irrigation season, indicating that the 

largest oxygen demand was coming from senescence 

of Aphanizomenon flos-aquae cells that are present 

in the Klamath River during the summer. However, 

during irrigation season in year 1, CBOD5 loads were 

lower than in the non-irrigation season, which may 

indicate that at times high concentrations of ammonia 

or cellular organic nitrogen leaving Upper Klamath 

Lake contribute a large nitrogenous oxygen demand as 

well.

• The smallest loads were computed for the farthest 

upstream sites in the Lost River Basin, suggesting 

that the upper Lost River Basin does not contribute 

substantial loads of TP, TN, BOD5, and CBOD5 to the 

Klamath Reclamation Project.
2 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

• Median concentrations of BOD5 and CBOD5 were 

lowest among the upper Lost River Basin sites and 

highest at site PPD (however, this comparison is 

based on only four samples collected at site PPD over 

the 3-year study). Median concentrations of BOD5

and CBOD5 also were elevated at sites KSDH (6.60 

and 4.70 milligrams per liter [mg/L], respectively) 

and KSD97 (4.47 and 3.45 mg/L, respectively). The 

highest maximum BOD5 and CBOD5 concentrations 

were reported at the Lost River Diversion Channel 

(39.0 and 26.5 mg/L, respectively) when water 

was flowing from the Klamath River toward the 

Klamath Reclamation Project, and site FMT (25.0 

and 23.9 mg/L, respectively), the study site at the 

southern end of Upper Klamath Lake. Carbonaceous 

oxygen demand, as represented by CBOD5, typically 

dominated the composition of the samples at all sites.

• The highest concentrations of dissolved organic carbon 

were present at sites KSDH (the headworks of Klamath 

Straits Drain) and KSD97 (Klamath Straits drain 

before it enters the Klamath River), and PPD (outlet of 

Tule Lake).

• Median concentrations of TN and TP at the upper Lost 

River Basin sites in years 1 and 2 were variable, but 

site MCRV showed a smaller range of values in those 

years compared to the other upper Lost River Basins 

sites, and an overall lower median concentration 

during irrigation seasons in years 1 and 2, suggesting 

that Gerber Reservoir does not contribute high 

concentrations of nutrients to the Lost River during 

irrigation season.

• Total Maximum Daily Load (TMDL) load allocations 

for TP and TN in Klamath Straits Drain were exceeded 

in all three study years. BOD5 load allocations were 

exceeded in years 1 and 2, but not year 3.

• TMDL load allocations for TP were exceeded in the 

Lost River Diversion Channel for all 3 years. Load 

allocations for TN were exceeded in year 1, but not in 

years 2 and 3. BOD5 loads were less than the TMDL 

load allocation for all three study years.

• The dearth of samples collected at the Klamath Straits 

Drain just downstream of the Lower Klamath National 

Wildlife Refuge did not allow for direct assessment of 

the Klamath Straits Drain acting as a nutrient source or 

sink. 

• TP, TN, BOD5, and CBOD5 loads estimated during 

the study period likely were smaller than long-term 

average conditions because of persistent drought 

conditions in the Upper Klamath Basin. The study 

results, therefore, fail to characterize loads from the 

Klamath Reclamation Project to the Klamath River 

that could be present in typical years, and suggest the 

need for load assessments during average or aboveaverage streamflow years. 

Introduction

Background

Water quality in parts of the Lost River and upper 

Klamath River is considered impaired with respect to 

dissolved oxygen, pH, chlorophyll-a (algae), and ammonia 

toxicity (Oregon Department of Environmental Quality, 

2017). In 2017, the Oregon Department of Environmental 

Quality (ODEQ) revised the 2010 Total Maximum Daily 

Load (TMDL) and Water Quality Management Plans for 

the Lost River and Upper Klamath Basins to establish 

water-quality goals for included waterbodies. The ODEQ 

established load allocations (amount of pollutant that point 

and nonpoint sources can contribute to the stream without 

exceeding State water-quality standards) for the TMDL 

for the Lost River Diversion Channel and Klamath Straits 

Drain, which represent drainage water to the Klamath River 

from irrigation lands within the Bureau of Reclamation 

(Reclamation) Klamath Reclamation Project (hereinafter, 

“Klamath Project” or “the project”). Reclamation manages 

water delivery to numerous irrigation districts within the 

project boundary. Nonpoint source load allocations were 

established for total phosphorus (TP), total nitrogen (TN), and 

the 5-day biochemical oxygen demand (BOD5).Additionally, 

load allocations for 5-day carbonaceous biochemical oxygen 

demand (CBOD5) and dissolved inorganic nitrogen were 

established for nonpoint sources within the Lost River Basin. 

These load allocations have a direct effect on the Klamath 

Project because Reclamation has a leading role in the storage, 

delivery, and management of water in the surrounding areas, 

and agricultural drains with nonpoint source load allocations 

originate within Klamath Project boundaries. 

In addition to the 2017 TMDL, a Biological Opinion 

(BO) addressing the effects of Klamath Project operations 

on endangered suckers and salmon from 2013 to 2023 was 

issued by the National Marine Fisheries Service and U.S. Fish 

and Wildlife Service in May of 2013 that required measures 

to assess and restore habitat for the endangered Lost River 

(Deltistes luxatus) and shortnose (Chasmistes brevirostris) 

suckers (National Marine Fisheries Service and U.S. Fish 

and Wildlife Service, 2013). The BO specifies improvements 

within a defined geographic area called the “Lost River 

Recovery Unit” based on species occurrence in Tule Lake, 

Clear Lake, and the Lost River, all waterbodies managed by 

Reclamation for irrigation deliveries.
Introduction 3

Purpose and Scope

This study was initiated by Reclamation in 2012 with the 

goals of computing a nutrient budget for the Klamath Project 

and to better characterize water quality in the Lost River 

and Klamath River Basins in Oregon for 3 years beginning 

in March 2012 and ending March 2015. Reclamation staff 

collected water-quality samples, field parameter data, and 

streamflow measurements from March 2012 to February 

2013, and the U.S. Geological Survey (USGS) collected 

water-quality samples, field parameter data, and streamflow 

measurements from March 2013 to March 2015. The 

objectives of this study were to calculate TP, TN, BOD5, and 

CBOD5 loads at specified sites within the Klamath Project. 

Sites were selected by Reclamation in year 1 of the study 

to allow for reach-scale assessments of constituent loads 

to determine if there was an increase or decrease in loads, 

and to determine the reasons for those differences (Jason 

Cameron, Bureau of Reclamation, oral commun., August 5, 

2016). Additionally, constituent concentrations were analyzed 

to identify spatial and temporal patterns in nutrient, organic 

carbon, and BOD5/CBOD5 concentrations. An improved 

understanding of water-quality loads in the Klamath River 

and Lost River Basins will provide important information 

for Reclamation in managing the Klamath Project for water 

quality.

Description of Study Area 

The Lost River Basin begins and terminates in a closed 

basin that straddles the Oregon-California border and covers 

parts of Klamath and Lake Counties in Oregon, and Modoc 

and Siskiyou Counties in California. The Basin is 7,790 km2

(3,009 mi2) in area, or 19.2 percent of the Upper and Lower 

Klamath Basins combined (Natural Resources Conservation 

Service, 2014). The Lost River headwaters are the tributaries 

to Clear Lake and the river terminates at Tule Lake. Along its 

course, the Lost River gains water from natural tributaries and 

gains and loses water by way of canals, drains, and pumps 

(fig. 1). The main stem of the Lost River is highly channelized 

and includes several impoundments to facilitate water storage 

and support diversion canals and return flow drains. 

Water in the upper Lost River Basin generally originates 

in Clear Lake and the Gerber Reservoir, and is diverted from 

Miller Creek through North Canal and from the Lost River 

main stem through West Canal during irrigation season (fig. 1). 

Water from these diversions returns to the Lost River main 

stem through agricultural drains. Harpold Dam (at site LRBH) 

marks the farthest downstream extent of water deliveries from 

these two reservoirs during irrigation season, except for about 

10 ft3/s that moves past the dam to service a small area that 

cannot be serviced by the A Canal (Jason Cameron, Bureau 

of Reclamation, oral commun., August 5, 2016). This area 

within the project, upstream of Harpold Dam, is commonly 

referred to as the east side of the Klamath Project. During 

non-irrigation periods, water in the Lost River moves freely 

from the upper Lost River Basin past Harpold Dam. 

During irrigation season, water is delivered from Upper 

Klamath Lake to multiple irrigation districts downstream 

of Harpold Dam. These districts are serviced by canals and 

laterals that originate from the A Canal, which conveys water 

from the southern end of Upper Klamath Lake. In the summer, 

Upper Klamath Lake has large blooms of cyanobacteria, 

which is dominated by the species Aphanizomenon flosaquae (AFA) (Eldridge and others, 2012). Site FMT (fig. 1), 

therefore, represents water-quality conditions caused by these 

algal blooms in the summer because of its location at the 

southern end of the lake, and also represents water diverted 

through A Canal during irrigation season. The algal bloom 

in the lake also causes water-quality issues downstream in 

the reach of the Klamath River between the Link River Dam 

and Keno Dam (Sullivan and others, 2010). As a result, water 

delivered to the Klamath Project through the Lost River 

Diversion Channel, North Canal, and Ady Canal also contains 

high concentrations of AFA, which can affect water quality in 

these canals.

An intricate system of canals, laterals, pumps, and 

drains services irrigation districts from Harpold Dam to Tule 

Lake, south of the Oregon border. Water in the Lost River 

downstream of the Lost River Diversion Channel originates 

in the Klamath River (through the Diversion Channel), from 

the Lost River main stem, and from various drains within 

nearby irrigation districts. The Lost River terminates at Tule 

Lake, and water from Tule Lake is intermittently pumped 

through Sheepy Ridge from Pump Plant D, into various 

management units within the Lower Klamath National 

Wildlife Refuge (NWR), and through the P-canal and 

associated laterals. Water from the Lower Klamath NWR 

moves through the Klamath Straits Drain adjacent to site 

KSDH on the Oregon-California border. In addition to water 

from the NWR, Klamath Straits Drain also receives drainage 

water from irrigated lands within the Klamath Drainage 

District (KDD), which does not receive water from A Canal 

diversions, but rather through North Canal and Ady Canal, 

which divert water directly from the Klamath River. (Note 

that North Canal and West Canal within KDD irrigated lands 

have identical names to the east side diversions.) Klamath 

Straits Drain terminates in the Klamath River upstream of the 

Keno Dam. 

During non-irrigation periods, water in the Lost River 

from the upper Lost River Basin is diverted to the Klamath 

River through the Lost River Diversion Channel, which is 

used for flood control during winter storms. Water in the 

Lost River between the Lost River Diversion Channel and 

Tule Lake originates from concrete box culvert drains that 

move stormwater from the city of Klamath Falls, and from 

drains from irrigation lands west and north of the Lost River 

Diversion Dam (Jason Cameron, Bureau of Reclamation, 

oral commun., August 5, 2016). The flow in the Lost River 

Diversion Channel is operated by gravity only, and water in 

the channel can flow to or from the Klamath River. 
4 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-1203_fig 01

Ady Canal

Lost River

Gerber

Reservoir 

Lost River

Tule Lake

Sump 1A

P Canal

P-1 Canal

Sump 1B

Lost River

Diversion

Channel

N Canal N Canal

North Canal

Upper

Klamath

Lake

P-1 Canal

Lower

Klamath

Lake

 A Canal

F Canal E Canal

G Canal

J Canal

C Canal

Center

Canal

Q Canal

R Canal

Link River

Lake

Euwana

Klamath River

B Canal

West Canal

North Canal

Mil el r Creek

D Canal

Lost River

M

Canal

West

Canal

Klamath 

Straits 

Drain

Clear Lake

OREGON

CALIFORNIA

HARPOLD

DAM

LINK

RIVER

DAM

KENO

DAM

LOST RIVER

DIVERSION

DAM

Sheepy

Ridge

MALONE

DIVERSION

DAM

NC

KRK

FMT

PPD

LRDC

LREW

MCRV

LRBM

LRBH

KSD97

ADC97

KSDH

Lower Klamath National Wildlife

Refuge boundary

EXPLANATION

Klamath Drainage District (KDD)Lost River Basin boundaryIndividual irrigation districtProject main canalDrain or lateralLost River Diversion ChannelKlamath Straits DrainSite with streamgageSite without streamgageFlow directionDam

LREW

Base from U.S. Geological Survey digital dataset, 30-meter digital elevation model, and other digital data, various scales. 

121°30' 122°

42°15'

42°41°45'

Canals, drains, and irrigation district data provided by Bureau of Recalamation.

0 2 4 6 8 10 MILES

0 2 4 6 8 10 KILOMETERS

OREGON

Klamath

Basin

Lost

River

Basin

CALIFORNIA

Figure 1. Sample and data collection sites, Klamath River and Lost River Basins, south-central Oregon and northern California, March 2012–March 2015. Sites KSD97 and ADC97 are located on Klamath Straits Drain and Ady Canal, respectively. Site locations are proximal to each other, resulting in the appearance of overlap on the map. See table 1 for site description details.
Methods 5

This study was done during water years1 (WYs) 2012–

15. Considering mean annual streamflow over a 40-year 

period (1976–2015) at the Williamson River near Chiloquin 

(USGS streamgage 11502500, the closest streamgage near 

the project area on an unregulated river), WY 2012 was 

considered a normal streamflow year with a mean annual 

streamflow close to the 50th percentile value for the 40-year 

period (fig. 2). WYs 2013–15 are all considered low-flow 

years, with mean annual streamflows below the 25th percentile 

of the 40-year period. Mean annual streamflow in WY 2014 

was below the 10th-percentile value. As a result, much of the 

data from this study were collected during abnormally low 

streamflow years, so interpretation of the results should be 

considered representative of these hydrologic conditions, and 

may not compare well to any future efforts that characterize 

normal streamflow years.

40

WY 2012

WY 2013

WY 2014

WY 2015

90th percentile

75th percentile

50th percentile

 (median)

25th percentile

10th percentile

Individual value below the

 10th percentile

Mean annual streamflow, in cubic feet per second, 1976–2015

0

500

1,000

1,500

2,000 EXPLANATION

32 Number of values

Individual value above the

 90th percentile

Figure 2. Mean annual streamflow at Williamson 

River near Chiloquin (U.S. Geological Survey 

streamgage 11502500), Upper Klamath Basin, southcentral Oregon, water years (WYs) 1976–2015, and 

reference lines for WYs 2012–15.

Methods

Sampling Sites

Water-quality samples, streamflow, and field parameter 

data were collected at 10 sites during year 1 of the study, 

and at 12 sites during years 2–3 (fig. 1, table 1). Reclamation 

collected all water-quality and field-parameter data during year 

1 (March 2012–March 2013), and the USGS collected data for 

years 2 and 3 (March 2013–March 2015) (table 2). Beginning 

in year 2, sites LREW and PPD were added by the USGS to 

represent water-quality conditions upstream of Tule Lake (site 

LREW), and at Pump Plant D (site PPD), which moves water 

from Tule Lake through Sheepy Ridge and into the P canal 

and associated laterals that eventually move water to Lower 

Klamath Lake, which is within the boundaries of the Lower 

Klamath NWR (fig. 1).

Three sites are used to represent conditions along 

the main Lost River Channel upstream of Tule Lake—

(1) below Malone Reservoir (site LRBM), (2) below Harpold 

Reservoir (site LRBH), and (3) Lost River at East-West 

Road (site LREW). Site PPD represents water that is pumped 

intermittently from Tule Lake through Sheepy Ridge. Two 

sites represent conditions along Lower Klamath Lake and the 

Klamath Straits Drain—(1) KSD headworks (site KSDH), and 

(2) Klamath Straits Drain at Highway 97 (U.S. Route 97) (site 

KSD97). Five sites represent tributaries to the Lost River, A 

Canal, and Klamath Straits Drain systems—(1) Miller Creek 

at Round Valley (site MCRV), (2) UKL at Fremont Bridge 

(site FMT, a surrogate for A Canal water quality), (3) North 

Canal (site NC), (4) Ady Canal at Highway 97 (U.S. Route 

97) (site ADC97), and (5) Lost River Diversion at Tingley 

Lane (site LRDC). The site at the Klamath River at Keno 

(KRK) is the lower boundary of the study area, and represents 

water quality on the main-stem Klamath River downstream 

of Upper Klamath Lake and the canals and drains managed 

by Reclamation that either divert or add water to the Klamath 

River (sites LRDC, NC, ADC97). 

1

The 12-month period from October 1, for any given year, through 

September 30 of the following year. The water year is designated by the 

calendar year in which it ends.
6 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015 Table 1. Water-quality sampling sites, Lost River Basin, south-central Oregon and northern California, March 2012–March 2015. [Site locations are shown in figure 1. Abbreviations: KDD, Klamath Drainage District; UKL, Upper Klamath Lake; UKR, Upper Klamath River] Site name Alternate site name Site name abbreviation USGS site identification No. Latitude (north) Longitude (west) Study years sampled Relevance Site group designation in current report Streamgage (yes or no) Lost River at Bridge Crossing below Harpold Dam Below Harpold Reservoir LRBH 421010121271200 42°10′10′′ -121°27′12′′ 1,2,3 Lost River main stem Upper Lost River sites no Lost River below Malone Reservoir Below Malone Reservoir LRBM 420025121132800 42°00′25.2′′ -121°13′27.6′′ 1,2,3 Lost River main stem Upper Lost River sites no Miller Creek at Round Valley none MCRV 421114121080100 42° 11′14.3′′ -121°08′1.3′′ 1,2,3 Lost River tributary inflow Upper Lost River sites no Lost River near Hatfield, California Lost River at East-West Road LREW 11488495 41°57′14′′ -121°30′12′′ 2,3 Lost River mainstem upstream of Tule Lake Tule Lake sites no Tulelake Canal at Sheepy Ridge Pumping Station Pump Plant D PPD 11488510 42°55′14′′ -121°33′58′′ 2,3 Connects Tule Lake to Lower Klamath Wildlife Refuge and Klamath Straits Drain Tule Lake sites no Ady Canal at Highway 97 none ADC97 11509200 42°04′51.3′′ -121°50′44.3′′ 1,2,3 Canal serving KDD KDD sites yes North Canal at Highway 97 North Canal NC 11509105 42°07′19.5′′ -121°49′43.5′′ 1,2,3 Canal serving KDD KDD sites yes Lost River Diversion at Tingley Lane none LRDC 11486990 42°10′04′′ -121°46′31′′ 1,2,3 Lost River tributary inflow or Klamath River tributary inflow KDD sites yes Klamath Straits Drain at Highway 161 near Dorris, California KSD headworks KSDH 415950121463701 41°59′50′′ -121°46′37′′ 1,2,3 Beginning of the Klamath Straits KDD sites no Klamath Straits Drain at Highway 97 none KSD97 420450121504500 42°04′50′′ -121°50′45′′ 1,2,3 Klamath Straits Drain mainstem downstream of all KDD drains KDD sites yes Fremont Bridge UKL at Fremont Bridge FMT 421420121481700 42°14′20′′ -121°48′17.1′′ 1,2,3 A-canal tributary inflow during irrigation season, and Klamath River inflow at south end of UKL End member no Klamath River at Keno, Oregon UKR downstream of Keno Dam KRK 11509500 42°08′00′′ -121°57′40′′ 1,2,3 Klamath River mainstem End member yes
Methods 7

Table 2. Study years and responsible sampling agencies.

[Sampling agency: Reclamation, Bureau of Reclamation; USGS, U.S. 

Geological Survey]

Study

year

Date

range

Sampling 

agency

Number

of sites

Year 1 03-27-12 to

03-10-13

Reclamation 10

Year 2 03-11-13 to 

03-09-14

USGS 12

Year 3 03-10-14 to

03-23-15

USGS 12

Collection of Water-Quality Samples

Water samples were collected every two weeks 

from March 2012 to March 2015, and were analyzed 

for concentrations of TP, TN, dissolved ammonia as N, 

(hereinafter, “NH3”), dissolved nitrate plus nitrite as N 

(NO3+NO2), dissolved orthophosphate as P (ortho-P), 

and chlorophyll-a. Samples also were collected for 

determination of BOD5 and CBOD5, which are the amount 

of dissolved oxygen needed by aerobic organoheterotrophic 

microorganisms to break down organic matter in the water 

sample during 5 days of incubation at 20 oC. CBOD5 differs 

from BOD5 in that the contribution from nitrogenous bacteria 

is suppressed during determination of CBOD5 (Delzer and 

McKenzie, 2003). Sites also were sampled about every 

8 weeks (beginning on April 22, 2013) for dissolved organic 

carbon (DOC), total particulate carbon (organic plus inorganic; 

TPC), and total particulate nitrogen (TPN) concentrations. 

As mentioned in the section, “Sampling Sites,” two 

different agencies were responsible for collecting waterquality samples over the 3-year study period. As a result, 

different sampling methods and analytical laboratories were 

used during sampling efforts by Reclamation during year 

1 compared to USGS during years 2 and 3. Reclamation 

collected grab samples in year 1 at all sites by using either a 

Van Dorn sampler or by hand-dipping a 14-L churn splitter 

into the stream depending on the site. The sampling devices 

were triple rinsed with environmental water prior to sample 

collection. Samples were processed on site using the churn 

splitter churned at a rate of 9 in/s for unfiltered samples. The 

1,000-mL, high-density polyethylene (HDPE) sample bottles 

were filled with churned water for analysis of Total Kjelhahl 

Nitrogen (TKN), TP, BOD5, and CBOD5. The 1,000-mL 

clear HDPE bottle for TKN and TP analysis was preserved 

with 1 mL of sulfuric acid. A 250-mL brown HDPE bottle 

was filled with churned water for chlorophyll-a analysis. 

After unfiltered samples were collected and preserved, filtered 

samples were collected from the water remaining in the 

churn splitter using a peristaltic pump and 0.45-micron (μm) 

inline filter. The 1,000-mL clear HDPE bottles were filled 

with filtered water for ortho-P, NH3, and NO2+NO3 analysis. 

The bottle for NH3 and NO3+NO2 analysis was acidified 

with 1 mL of sulfuric acid. All water samples were chilled 

on-site and during transport. Nutrient and BOD5/CBOD5

samples were shipped overnight on ice to the Sierra Foothills 

Laboratory (no longer in operation) for analysis. Whole water 

for chlorophyll-a was shipped overnight to the Reclamation 

Pacific Northwest Regional Laboratory in Boise, Idaho, 

where it was filtered prior to analysis. Field parameters (water 

temperature, dissolved oxygen, pH, and specific conductance) 

were collected using a YSI® multi-parameter sonde after 

sample collection, and a secchi depth was recorded. Turbidity 

data also were recorded using a separate HACH® turbidimeter. 

Analytical methods and reporting limits for the project are 

shown in table 3.

Samples collected by USGS in years 2–3 of the study 

were collected following established USGS sampling 

protocols (U.S. Geological Survey, various dates) and using 

USGS-certified field supplies that are subject to qualityassurance procedures. When flows at the sampling sites 

exceeded 0.46 m/s (1.5 ft/s), samples were collected using 

the equal-width-increment (EWI) method as described in the 

USGS Field Manual (U.S. Geological Survey, 2006). The 

EWI method results in a composite sample that represents the 

streamflow-weighted concentration of analytes in the stream 

cross section being sampled. Samples were collected as grab 

samples when flows were less than 0.46 m/s (1.5 ft/s). These 

grab samples were collected in an open container, a DH-81 

water-quality sampler, or a DH-95 water-quality sampler, 

without a nozzle and from a single point in the stream cross 

section. Where possible, grab samples were collected from 

several locations across the channel and combined in one 

sample.

Water samples collected by the USGS were composited 

using an 8-L churn splitter. TP and TN samples were preserved 

immediately after collection with the addition of 1 mL of 4.5 

normal (4.5 N) sulfuric acid, and dissolved nutrient samples 

were filtered through a 0.45-μm capsule filter. All water 

samples were chilled on site and during transport. Total and 

dissolved nutrient samples were shipped on ice overnight 

within 3 days of collection and analyzed at the USGS National 

Water Quality Laboratory (NWQL; Denver, Colorado). 

Analytical methods and method reporting limits for USGS 

sample collection are shown in table 3. Dissolved nutrient 

samples were analyzed using USGS methods I-2525-89 

and I-2522-90 for NH3 concentration, method I-2545-90 

for NO2+NO3 concentration, and methods I-2606-89 and 

I-2601-90 for ortho-P concentration (Fishman, 1993). TP and 

TN samples were analyzed using USGS method I-4650-03 

(Patton and Kryskalla, 2003). Water samples collected for 

chlorophyll-a analysis were passed through 47-mm-diameter, 

1.2-μm pore size, glass-fiber (WhatmanTM GF/C) filters 

(Whatman, Inc., Piscataway, New Jersey) at the USGS 

Klamath Falls Field Station and immediately frozen. 
8 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015 Table 3. Laboratory analysis methods and method reporting limits for this study, March 2012–March 2015.

[Abbreviations: BOD, biochemical oxygen demand; BOR-PNRL, Bureau of Reclamation Pacific Northwest Regional Laboratory; CBOD, carbonaceous biochemical oxygen demand; Chl-a, chlorophyll-a; DOC, dissolved organic carbon; EPA, U.S. Environmental Protection Agency; MRL, method reporting limit; N, nitrogen; NWQL, National Water Quality Laboratory; P, phosphorus; TPC, total particulate carbon; TPN, total particulate nitrogen; SM, standard method; SRWQL, Sprague River Water Quality Laboratory; USGS, U.S. Geological Survey; mg/L, milligram per liter; NA, not applicable]]

Project Year 1, Bureau of Reclamation Project Years 2–3, U.S. Geological Survey

Analyte Analyzing laboratory Analytical method MRL (mg/L) Analyte Analyzing laboratory Analytical method MRL (mg/L)

Total P as P, unfiltered Sierra Foothills SM 4500P-E 0.020 Total P as P, unfiltered NWQL USGS I-4650-03 0.010Total Kjeldahl nitrogen as N, unfiltered Sierra Foothills SM 4500NH3C/351.2 0.20 Total nitrogen as N, unfiltered NWQL USGS I-4650-03 0.050Orthophosphate as P, filtered Sierra Foothills EPA 365.3/SM 4500P E 0.050 Orthophosphate as P, filtered NWQL USGS I-2606-89, I-2601-90 0.004Ammonia as N, filtered Sierra Foothills SM 4500NH3B,D/350.1 0.030 Ammonia as N, filtered NWQL USGS I-2525-89, I-2522-90 0.010Nitrate + nitrite as N, filtered Sierra Foothills SM 4110B/EPA 300.0 0.050 Nitrate + nitrite as N, filtered NWQL USGS I-2545-90 0.050BOD Sierra Foothills SM 5210B 2.0 BOD SRWQL SM 5210B 0.30CBOD Sierra Foothills SM 5210B 2.0 CBOD SRWQL SM 5210B 0.30Chl-a BOR-PNRL SM 10200H various Chl-a BOR-PNRL SM 10200H variousDOC NA NA NA DOC NWQL USGS O-1122-92 0.23TPC NA NA NA TPC NWQL EPA 440.0 0.050TPN NA NA NA TPN NWQL EPA 440.0 0.030
Methods 9

These samples were stored and analyzed according to 

Standard Method 10200H (American Public Health 

Association, 2005) at the Bureau of Reclamation Pacific 

Northwest Region Laboratory in Boise, Idaho. Samples for 

BOD5 and CBOD5 analysis were delivered the same day they 

were collected to the Sprague River Water Quality Laboratory 

(SRWQL) in Chiloquin, Oregon. The close proximity of this 

laboratory to the study area allowed for minimal holding 

time (6–24 hours) between sample collection and the start of 

analysis. Samples were analyzed at the SRWQL following 

standard method 5210B (Clesceri and others, 2005).

Samples collected every 8 weeks for determination 

of DOC, TPC, and TPN concentrations were filtered at the 

Klamath Falls Field Station the same day they were collected 

using pre-combusted 25-mm-diameter, 0.7-μm pore size, 

glass fiber (WhatmanTM GF/F) filters and following the USGS 

procedures for processing water samples (Wilde and others, 

2004). For DOC samples, the filtrate was submitted for 

analysis, and for TPC/TPN samples, the filtrand was analyzed. 

Samples were shipped on ice overnight within 3 days of 

collection and analyzed at the USGS NWQL. DOC samples 

were analyzed following USGS method O-1122-92 (Brenton 

and Arnett, 1993), TPC and TPN were analyzed using U.S. 

Environmental Protection Agency method 440.0 (Zimmerman 

and others, 1997).

In year 1 of the study, water samples collected by 

Reclamation were analyzed for TKN, whereas, in years 2 and 

3, USGS samples were analyzed for TN. These two analytes 

are not equivalent, as Kjeldahl nitrogen includes ammonium 

and organic nitrogen, whereas TN includes ammonium, 

NO3+NO2, and organic nitrogen (Patton and Kryskalla, 2003). 

Therefore, TN reported for year 1 of this study was calculated 

by adding the nitrate plus nitrite results to the TKN results 

and the resulting TN values were flagged as “estimated” in the 

USGS National Water Information System database.

Streamflow Data

Instantaneous streamflow for each sample event was 

determined from the continuous streamgage located at the 

sampling site, or, for sites without a continuous streamgage, 

an instantaneous streamflow measurement was collected 

during each sample event. At sites without a streamgage, 

instantaneous flow measurements were determined by 

two methods—(1) the mid-section method as described in 

Turnipseed and Sauer (2010) and (2) the moving boat method 

using an acoustic Doppler current profiler (Simpson, 2001, 

Turnipseed and Sauer, 2010). Streamflow primarily was 

determined using the mid-section method at sites LRBM, 

MCRV, LRBH, and LREW, and the moving boat method was 

used twice at site LRBH and once at site LREW. The moving 

boat method also was used for streamflow measurements at 

sites FMT, PPD, and KSDH. 

Streamflow data were recorded continuously at sites 

LRDC, NC, ADC97, KSD97 and KRK. Instantaneous 

streamflow was computed at sites LRDC, NC, ADC97, 

and KSD97 using the index velocity method described 

in Levesque and Oberg (2012). At site KRK, the stagestreamflow method was used. The stage-streamflow method 

is based on the relation between channel water level (stage), 

as measured by an in-place sensor, and streamflow for a 

range of conditions. Streamflow relations were checked with 

instantaneous streamflow measurements every 6–8 weeks. 

Site FMT is located at the southern end of Upper 

Klamath Lake, just upstream of the Link River Dam and the 

A Canal diversion. The lake is constricted at site FMT, and 

water is diverted through the A Canal and the Link River Dam 

downstream of the site, so measurable streamflow occurs 

at site FMT year-round. However, streamflow at site FMT 

often is affected by wind events and can change rapidly. 

The outflow from Upper Klamath Lake at site FMT was not 

directly measured from the start of the study in March 2012 to 

July 29, 2013. Instantaneous streamflow was estimated at this 

site using the water balance from data recorded at the USGS 

streamgage on the Link River, located 2.1 km downstream 

of Fremont Bridge (USGS streamgage 11507500, fig. 3), and 

flow data provided by Bureau of Reclamation for A Canal and 

Pacific Power for the Westside Canal (also known as “Keno 

Canal”). The water-balance equation was the sum of the flows 

out of Upper Klamath Lake through the A Canal, the Westside 

Canal, and the Link River. Instantaneous streamflow measured 

after July 29 were compared to the water-balance-calculated 

instantaneous streamflow, and the estimated streamflow values 

were determined to be reasonable (median relative percentage 

difference, 4.6 percent; range, 0.0–26 percent). The Eastside 

Canal was not included in the calculation because that 

streamflow was included in Link River streamflow.

Load Estimation

Constituent loads were computed at all project sites for 

TP, TN, BOD5, and CBOD5. Loads were computed using 

two methods: (1) a multivariate regression load estimation 

program, and (2) computation of instantaneous loads for 

individual samples averaged over specified time periods 

during the study. 
10 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-1203_fig 03

Link River Dam

Site FMT (Fremont

Bridge)

Link River

Link River streamgage Eastside Canal

Westside Canal

2.1 km

Upper Klamath Lake

A Canal

Figure 3. Schematic representation of the Link River 

(connecting Upper Klamath Lake to Lake Ewauna) 

showing flows (arrows) used to estimate instantaneous 

streamflow at site FMT, Upper Klamath Basin, southcentral Oregon. Total flow at site FMT was determined 

as the sum of flows from A Canal, Westside Canal, and 

the Link River. Flow data from A Canal and Westside 

Canal were provided by the Bureau of Reclamation and 

Pacific Power; flow on the Link River was measured 

by the U.S. Geological Survey streamgage 11507500, 

located 2.1 kilometers downstream of Fremont Bridge. 

Site name and description are shown in table 1; site 

location is shown in figure 1.

LOADEST Models

The USGS LOAD ESTimator (LOADEST) program 

(Runkel and others, 2004), a USGS program for estimating 

constituent loads in streams and rivers, was used to estimate 

loads at two of the project sites that represent the upper 

and lower boundaries of the study—(1) the northernmost 

project site at Fremont Bridge (site FMT), and (2) the 

southernmost project site at Klamath River downstream 

of Keno dam (site KRK). The R-version of LOADEST 

(rloadest), an update from the Fortran-based model described 

by Runkel and others (2004), was used to run the models for 

this study. LOADEST uses a multiple regression approach to 

estimate the effects of streamflow, season, and time on waterquality concentration and loads. LOADEST models were not 

able to be calibrated at other sampling sites in the study area 

because consistent relations among flow conditions and waterquality constituent concentrations could not be identified. 

LOADEST includes several predefined models that 

specify the form of a multivariate regression equation to 

estimate loads, using explanatory variables of streamflow, 

time, and season. The base model used in this study is shown 

in equation 1, with six explanatory variables plus an intercept 

term. The primary method used to estimate parameters in the 

regression equation within LOADEST is adjusted maximum 

likelihood estimation (AMLE), except for the special cases 

where the calibration data set is uncensored, in which case 

maximum likelihood estimation (MLE) is used (Runkel 

and others, 2004). The AMLE and MLE methods assume a 

linear model with normally distributed errors; logarithmic 

transformations are frequently used to satisfy the normality 

assumptions and to improve the fit of the regression (Helsel 

and Hirsch, 2002). LOADEST users can select a predefined 

model based on the knowledge of the system being modeled, 

or the program can select a best-fit model using an automated 

process that incorporates two statistics to select the model—

the Akaike Information Criterion (AIC) and the Schwarz 

Posterior Probability Criterion (SPPC) (Runkel and others, 

2004). The two statistics are computed for the calibrated 

model, and the predefined model with the lowest AIC statistic 

is selected as the best-fit model by the program, which 

contains some combination of the explanatory variables 

shown in equation 1. For this study, the best-fit model was 

evaluated, as well as additional models with the next-lowest 

AIC statistics:

2

12 3 4

2

56 7

ln( )= (ln ) (ln )

sin(2 ) cos(2 )

L Q Q dtime

dtime dtime dtime

β +β × +β +β ×

+ β × + β π + β × π , (1)

where

ln is natural logarithm;

L is constituent load in kilograms per day;

β1...7 are coefficients of the explanatory variables;

Q is streamflow, in cubic feet per second; and 

dtime is decimal time.

In addition to the AIC-determined model selection 

approach, seasonal-wave load models also were evaluated 

to determine if that model type resulted in a better-fit model 

than the model form in equation 1. A seasonal wave function 

has been shown to work well for pesticide models (Vecchia 

and others, 2008), where concentrations follow seasonal 

patterns unrelated to streamflow. Seasonal wave models, 

therefore, were evaluated given the seasonal pattern of the 

irrigation season, and the seasonal patterns of total nutrient 

concentrations in Upper Klamath Lake. The seasonal-wave 
Methods 11

model requires determining the timing of the peak of the 

constituent loads and values for the other parameters of 

the model, which comprise a loading period and decay rate 

(Lorenz, 2017). The form of the seasonal-wave model is 

shown in equation 2:

( ) ( ( ))

( )

ln center ln

seasonalWave , , ,

L Q

dtime p l d

=β+

+ , (2)

where

ln is natural logarithm;

L is constituent load in kilograms per day;

β is Intercept term;

Q is streamflow, in cubic feet per second;

dtime is decimal time;

p is timing of the constituent concentration 

peak, in decimal time;

l is loading period, in months; and

d decay rate indicated by a half-life, in months.

The center (ln(Q)) term in equation 2 is referred to as a 

streamflow anomaly by Vecchia and others (2008), which is 

the deviation of concurrent daily streamflow from average 

conditions for the previous 30 days. The “seasonalWave” term 

is a function in R that describes the variation in ln (L) over the 

course of a year as a function of the remaining explanatory 

variables. Documentation for this and other USGS-specific 

R functions in rloadest can be found at https://github.com/

USGS-R/rloadest.

Several model statistics were evaluated when selecting 

the final model to estimate constituent loads:

1. The coefficient of determination (R2),

2. The probability plot correlation coefficient (PPCC),

3. The load bias in percent (Bp),

4. The partial load ratio, and

5. The Nash Sutcliffe Efficiency Index.

The PPCC value tests the normality of residuals on a normalprobability plot, and log-transformations that maximize the 

PPCC value (correlation coefficient values close to 1) for 

regression residuals optimize the normality of the residuals 

(Helsel and Hirsch, 2002), which satisfies the assumptions of 

multivariate linear regression. LOADEST includes routines 

to identify the best model from a suite of models based on the 

lowest AIC score (Runkel and others, 2004). In some cases, 

the model with the PPCC value closest to 1 or the lowest 

Bp value may not have been the model with the highest R2

or the lowest AIC. As a result, the model that was used to 

estimate loads in this study may have required rejecting the 

best-fit model selected by LOADEST if the best-fit model was 

shown to have more bias or did not satisfy the assumptions 

of the regression as well as a different model. Seasonal wave 

models are not incorporated in the AIC and SPPC process of 

model selection within the program, so those models were 

run separately and the model statistics were evaluated in 

comparison to the multivariate regression model results. The 

seasonal wave model in LOADEST also does not function 

with left-censored data, so this model type was evaluated first 

for TP and TN loads, which did not contain censored results 

for sites FMT and KRK. BOD5 and CBOD5 models for both 

sites were evaluated using the multivariate models explained 

above. If the multivariate model for BOD and CBOD was 

determined to be unsatisfactory, the seasonal wave model was 

evaluated, and left-censored data were treated as results with 

concentrations that were equal to the laboratory reporting 

limit.

The LOADEST program was run on the current R 

platform as developed by the USGS, which includes updates 

in 2013 that provided additional diagnostic tools to evaluate 

bias in models estimating constituent loads. The 2013 update 

is available at http://water.usgs.gov/software/loadest/doc/

loadest_update.pdf. 

Daily constituent loads calculated using LOADEST 

were aggregated for irrigation and non-irrigation seasons for 

each year of the study by averaging the daily loads. Irrigation 

seasons for sites FMT and KRK were defined as the time 

period when water was diverted through A Canal.

Instantaneous and Daily Load Averaging

Surface water constituent loads at study sites without 

continuous records of streamflow, or for those sites that were 

located on Reclamation project canals where LOADEST 

was not used, were computed as instantaneous loads for each 

sample date when there was measurable streamflow at the 

site. When there was no measurable streamflow at the site, the 

instantaneous load was assumed to be zero and incorporated in 

the overall average. Instantaneous loads were computed using 

equation 3:

L C Q c i = × × , (3)

where

Li is instantaneous load in kilograms per day;

C is constituent concentration in milligrams per 

liter;

Q is streamflow, in cubic feet per second (ft3/s) 

or cubic meters per second (m3/s); and

c conversion factor = 2.45 for Q in ft3/s, and 

86.4 for Q in m3/s.

Instantaneous streamflow measurements were collected 

on sample days at site locations that were not located on 

Reclamation canals within the Klamath Project, following 

methods described in the section, “Streamflow Data”. The 

concentrations of TP, TN, BOD5, and CBOD5 were multiplied 

by these instantaneous streamflow measurements, and used 
12 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

to compute instantaneous loads using equation 3. Study 

sites with only instantaneous streamflow data used for load 

calculations include sites LRBH, LRBM, MCRV, KSDH, 

LREW, and PPD. Sample data collected at site MCRV 

in year 1 by Reclamation did not include instantaneous 

streamflow measurements, but instead relied on an existing 

rating curve operated by Reclamation for flows coming out 

of Gerber Reservoir, just upstream of the sampling site. 

As a result, instantaneous loads for year 1 at site MCRV 

were calculated using daily streamflow values provided by 

Reclamation, and loads for years 2 and 3 were calculated 

using the instantaneous streamflow measurements collected by 

USGS during sample collection. In study year 1 at site MCRV, 

Reclamation reported zero flows during non-irrigation periods, 

so the loads are assumed to be zero for that time period. For 

years 2 and 3, USGS recorded measurable streamflow from 

instantaneous measurements during non-irrigation periods, so 

loads are reported for those time periods.

At the canal sites (sites KSD97, NC, ADC97, and 

LRDC), daily values of streamflow obtained from the 

streamgage data were used to compute daily loads. Daily 

values were used at these sites because there were numerous 

scenarios where water-quality samples were collected at 

very low or very high streamflows that were the result 

of intermittent pump operations throughout the day. The 

instantaneous streamflows during sample collection often 

did not accurately represent the flow regime for the day, 

potentially resulting in non-representative daily loads. This 

approach requires the assumption that the samples collected 

at a discrete point in time also represented water-quality 

conditions for that day. In subsequent sections of this report, 

daily and instantaneous loads at the canal sites are referred to 

as instantaneous loads.

Loads were aggregated each study year by averaging all 

the calculated daily loads during irrigation and non-irrigation 

seasons. In subsequent sections of this report, the “load” at 

a site refers to this aggregated value, unless explicitly stated 

otherwise. For sites FMT and KRK, where LOADEST was 

used to compute loads, daily loads computed from the model 

were averaged separately for irrigation and non-irrigation 

seasons. This resulted in two average loads per study year per 

site, for a total of six time periods over the three study years. 

Irrigation season lengths were different for sites on the 

western side of the project receiving water from A Canal 

diversions compared to sites on the eastern side of the project 

receiving water from Clear Lake and Gerber Reservoir. As 

a result, the length of the irrigation season for the western 

sites was defined as the time period when water was diverted 

through A Canal—typically mid-April to early October. 

The length of the irrigation season for the eastern sites also 

typically was mid-April to early October, and was defined 

as the time period when water was diverted from Gerber 

Reservoir (for sites MCRV and LRBH), and when water was 

diverted through the West Canal (for site LRBM) (fig. 1).

Quality Assurance 

Because two agencies collected water-quality samples 

that were analyzed at different laboratories, reporting of 

quality assurance (QA) results is separated by the collecting 

agency.

Bureau of Reclamation Quality Assurance

QA samples were collected at various sites by 

Reclamation during the first year of the study. Sample QA 

followed standard operating procedures specific to the 

Klamath Basin Area Office of the Bureau of Reclamation. In 

summary, these samples included blanks and field duplicate 

samples. Blank samples were collected as laboratory blanks or 

rinsate blanks as denoted by Reclamation standard operating 

procedures. Laboratory blanks were prepared in the laboratory 

or office to avoid field contamination for the purpose of 

testing the cleanliness of the sampling equipment. Laboratory 

blank sample bottles were rinsed three times with reagent 

grade deionized (DI) water and corresponding preservatives 

were added. A rinsate blank is designed to check sampling 

equipment and field crew techniques for contamination. After 

the sampling equipment had been cleaned with DI water 

at the last sampling site of the day, the rinsate blank was 

collected. Rinsate blanks were prepared by pouring reagent 

grade DI water into the sample collection equipment (Van 

Dorn, etc.), ensuring that all internal surfaces are wetted. The 

rinsate water was then collected in a churn splitter. Following 

field procedures, the sample bottles were rinsed three times 

with the rinsate water and then filled with rinsate water. For 

filtered constituents, the rinsate water was filtered using a 

peristaltic pump or filter syringe using the same techniques 

that were used for the regular sample. Preservation techniques 

are the same as those used for the regular samples. Duplicate 

samples were subsamples of the total sample, had a water 

matrix identical to that of the regular sample, and were used to 

determine analytical precision within an analyzing laboratory.

U.S. Geological Survey Quality Assurance

QA samples were collected at various sites by USGS 

during the second and third years of the study. These samples 

included the following:

1. Field equipment blanks (the first samples collected each 

sample day in the field) for total (TP, TN) and dissolved 

nutrients (NH3, NO3+NO2, ortho-P), BOD5, CBOD5, 

and DOC,

2. Laboratory equipment blanks (collected at the Klamath 

Falls Field Station prior to field sampling on days with 

inclement weather—three times for total and dissolved 

nutrients and once for BOD5, CBOD5, and DOC during 

the study period,
Quality Assurance 13

3. Laboratory filtration blanks (collected after samples 

were filtered at the Klamath Falls Field Station for TPC, 

TPN, and chlorophyll-a), and

4. Either a sequential replicate sample (hereinafter, 

“replicate” sample) or a split replicate sample 

(hereinafter, “split” sample) for all constituents.

The laboratory filtration blank described in item number 3 is a 

process to test the efficiency of cleaning procedures between 

environmental samples that are filtered for particulate carbon 

and nitrogen, and chlorophyll-a.

Replicate environmental samples were collected twice 

in rapid succession from the same location (the entire sample 

collection procedure was completed twice), and analyzed 

to determine variability associated with sample collection 

procedures and analytical methods. Split samples were 

environmental samples collected once and divided into two 

or more samples (analysis bottles were filled sequentially 

from the same churn splitter) to determine the variability in 

sample splitting and in the analytical methods. Split samples 

were collected in addition to replicates to determine how 

much variability measured in replicate samples was due to 

sampling compared to laboratory analysis. Blank spike and 

sample matrix spike samples also were prepared for total 

and dissolved nutrient analyses to measure potential bias 

in laboratory analytical procedures. Spike samples were 

prepared at the USGS Klamath Falls Field Station by adding 

target compounds (a field-matrix spike mixture) to American 

Chemical Society reagent-grade inorganic blank water and to 

split-replicate environmental samples. Methods for collecting 

and evaluating quality-control samples are described in 

Eldridge and others (2012).

Quality Assurance Results

Bureau of Reclamation Quality 

Assurance Results

Blank sample results from Reclamation in year 1 of the 

study (March 2012–February 2013) showed no occurrences 

exceeding the minimum reporting level (MRL) for TP, TKN, 

ortho-P, NH3, and NO3+NO2 (table 4a). The MRL for TKN 

changed from 0.20 to 0.05 mg/L on January 15, 2013, and 

blank sample concentrations beyond that date also were less 

than the new MRL. All chlorophyll-a filter apparatus blanks 

and BOD5/CBOD5 field blank concentrations also were less 

than the laboratory reporting limits for all blank samples.

Table 4. Quality-control data for Bureau of Reclamation 

water-quality samples, Klamath River and Lost River drainages, 

south-central Oregon and northern California. (a) blank samples, 

March 2012–March 2015; (b) replicate samples, March 2013–

March 2014.

[Table 4a and 4b are Microsoft® Excel files and are available for download at 

https://doi.org/10.3133/sir20185075]

The mean relative percent difference (RPD) for all 

duplicate samples was less than 10 percent for TP, ortho-P, 

NH3, NO3+NO2, and BOD5/CBOD5 (table 4b). The mean 

RPDs for chlorophyll-a and TKN duplicates were 14.8 and 

14.9 percent, respectively.

U.S. Geological Survey Quality 

Assurance Results

Less than 5 percent of all blank samples for total 

nutrients (TP and TN, n=106), dissolved nutrients (ortho-P, 

NH3, NO3+NO2, n=106), chlorophyll-a (n=105), and DOC 

(n=24) contained concentrations more than the minimum 

reporting level (table 5a). Laboratory filtration blank samples 

for TPC and TPN analyses exceeded the MRL in 17 and 9 

percent of samples, respectively. However, concentrations of 

TPC and TPN in environmental samples were much greater 

than the concentrations detected in the blank samples. Mean 

concentrations in laboratory filtration blank samples were 

0.20 and 0.04 mg/L for TPC and TPN, respectively, whereas 

the fifth-percentile values of environmental samples collected 

at all sites exceeding the MRL were 0.51 and 0.06 mg/L for 

TPC and TPN, respectively (table 5a). Therefore, low-level 

contamination indicated by the blanks did not limit the use of 

these data. 

Table 5. Quality-control data for U.S. Geological Survey 

water-quality samples, Klamath River and Lost River drainages, 

south-central Oregon and northern California. (a) blank samples, 

March 2012–March 2015; (b) split samples, March 2012–March 

2015; (c) replicate samples, March 2013–March 2014; (d) spikes, 

March 2013–March 2014. 

[Tables 5a, 5b, 5c, and 5d are Microsoft® Excel files and are available for 

download at https://doi.org/10.3133/sir20185075]

Fifty-three percent of BOD5 and 58 percent of CBOD5

equipment field blank samples and the single laboratory 

equipment blank sample for BOD5 and CBOD5 exceeded the 

MRL. Contamination in these blank samples was primarily 

an artifact of the process used to initiate the blank water 

incubation for the assay, and, therefore, an overestimate of 

contamination in the environmental samples. Laboratory 

personnel informed USGS that the initial dissolved oxygen 

readings of submitted blank water samples typically were 

supersaturated and that the initial agitation of the sample 

was ineffective at bringing the concentration to saturation. 

As a result, over a 5-day analysis, the blank water would 

equilibrate to laboratory conditions and lose a portion of its 

dissolved oxygen, resulting in the sample analysis at 5 days 

showing depletion of dissolved oxygen and a value greater 

than the reporting limit. Once the problem was rectified, 

the concentration in the blank samples decreased (table 5a). 
14 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

BOD5 and CBOD5 concentrations measured in environmental 

samples generally were much larger than the concentrations 

detected in the blanks. The mean concentration of BOD5

and CBOD5, measured in equipment blank samples with 

concentrations greater than the MRL, was 0.61 mg/L (range 

0.30–2.69 mg/L) and 0.62 mg/L (range 0.30–2.40 mg/L), 

respectively, for equipment field blanks, and 1.20 and 

1.22 mg/L, respectively, for laboratory equipment blanks 

(only one laboratory equipment blank was collected). The 

5th-percentile values of environmental samples (collected 

from the same sites as the field equipment blanks) for BOD5

and CBOD5 were 1.21 and 0.90 mg/L, respectively (table 5a). 

Therefore, low-level contamination indicated by the blanks did 

not limit the use of these data. 

Split and replicate samples collected during March 

2013–March 2015 had mean RPDs of less than 11 percent 

for all dissolved nutrients and DOC (tables 5b and 5c), 

with greater RPD values for replicate samples than for split 

samples, indicating the greater variability associated with 

sequential sampling. The RPD of split samples of analytes 

with suspended material generally was higher than the RPD of 

replicates sampled for the same analytes, suggesting that the 

sample splitting (using a churn splitter) did not provide much 

uniformity in samples with regard to suspended material. 

The highest RPDs for split samples of suspended material 

were reported for BOD5 and CBOD5 (11.2 and 15.1 percent, 

respectively), the next highest for chlorophyll-a (11.1 percent), 

and the third highest for TPN (10.5 percent). 

Bias measured by analysis of spike samples is known 

as “recovery,” which is a measure of a spike analyte added 

to a sample, expressed as the percentage of the spiked 

amount (U.S. Geological Survey, 2006). The recovery in a 

sample without loss or gain of the measured analyte (due 

to degradation or matrix character) should be 100 percent. 

Spiked nutrient samples for this study were prepared and 

analyzed on July 17, 2013, December 3, 2013, and July 17, 

2014. The results showed mean nutrient spike recoveries 

between 92 and 103 percent for the July and December 2013 

spikes (table 5d), and 75 to 164 percent for the July 2014 

spike. With the exception of the 2014 spiked samples, all 

recoveries were greater than 90 percent and most were greater 

than 96 percent. The maximum (164 percent) and minimum 

(75 percent) recoveries for the July 2014 spiked samples 

all occurred in the mid-level spiked blank water and spiked 

sample matrix water, respectively, for NO3+NO2. These low 

and high recoveries likely originated from a pipet error during 

spike sample preparation because mean recovery for low-level 

and high-level spiked blank water was 101 and 97 percent, 

respectively.

Results

Streamflow

As mentioned in the section, “Background,” streamflow 

in the Upper Klamath Basin was below average for most of the 

study period, particularly during WYs 2014 and 2015 (fig. 2). 

The sites with the highest streamflow for all three study years 

during both irrigation and non-irrigation seasons were the 

end member sites FMT and KRK (fig. 4). Average streamflow 

ranged from 1,440 to 2,200 ft3/s at FMT during irrigation 

season, and 653 to 715 ft3/s during non-irrigation season. By 

comparison, all the other study sites except for KRK had mean 

streamflows of less than 200 ft3/s for both irrigation and 

non-irrigation seasons. Streamflow data during irrigation and 

non-irrigation seasons in year 1 were not recorded for sites 

LREW and PPD, and were not available for site KSDH. In 

non-irrigation year 2 and all of study year 3, streamflow at 

site KSDH was determined to be zero, which also resulted in 

zero values for constituent loads. (Note that mean streamflow 

data for sites LREW and PPD during irrigation seasons 2 and 

3, and site MCRV during non-irrigation seasons do not appear 

in figure 4 because the values are too small to appear on the 

scale of the bar chart, which is scaled to the same value on 

the y-axis to allow for comparison between sites.) Among the 

upper Lost River Basin sites, site MCRV had the highest mean 

streamflow during irrigation season, a result of dam releases 

from Gerber Reservoir for irrigation. During non-irrigation 

periods, site LRBH had the highest streamflow among those 

sites, a result of the management of streamflow that allows 

water to pass through the small regulating structure during 

non-irrigation periods. 

Water-Quality Concentrations

For purposes of this report, only those water-quality 

samples collected while there was measurable streamflow at 

the sampling site are reported. At site LRDC, where water 

flows in two directions depending on water management 

operations and season, a positive flow direction [LRDC(+)] 

indicates water flowing from the Klamath River onto the 

Klamath Project, and a negative flow direction [LRDC(‐)] 

indicates water flowing from the project toward the 

Klamath River. This designation is consistent with water 

velocity directional data recorded at the streamgage where 

samples were collected as mentioned above. Eleven sample 

concentrations are reported for site KSDH over the 3-year 

study; however, only two of these samples were used to 

compute instantaneous loads. The additional nine samples 

are from year 1 of the study when Reclamation collected 

samples and the site was flowing, and during irrigation year 2. 
Results 15

tac18-1203_fig 04

Site

Mean streamflow, in cubic feet per second

End member sites Upper Lost River Basin sites Tule Lake sites

0

500

1,000

1,500

2,000

2,500

0

500

1,000

1,500

2,000

2,500

FMT KRK LRBH LRBM MCRV LREW PPD ADC97 KSD97 KSDH LRDC NC

Klamath Drainage District sites

Irrigation season

Non-irrigation season

Irrigation season

Non-irrigation season

Irrigation season

Non-irrigation season

Irrigation season

Non-irrigation season

Year 2

Year 3

Year 1

EXPLANATION

Figure 4. Mean streamflow at study sites during irrigation and non-irrigation seasons, Klamath River and Lost River Basins, 

Oregon and California, March 2012–March 2015. Site names and descriptions are shown in table 1; site locations are shown in 

figure 1.
16 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

Streamflow values during these periods could not be verified 

to compute instantaneous loads, so those values were not 

included in the load computations.

A Mann-Whitney U test was done on the sample 

concentration results to determine if mean concentrations 

of constituents were distinguishable between sites (p<0.05). 

In tables 6 and 7, the “MWU” column contains results of 

these analyses in the form of lowercase letters. Sites that 

share a letter have sample concentrations that are statistically 

the same, and sites that do not share a letter have sample 

concentrations that are not statistically the same. This test 

was not used on DOC, TPC, and TPN results because the 

small sample sizes (n<13) did not allow for robust statistical 

analysis.

Total Nutrients

The highest median concentrations of TP from the three 

study years at all sites were at site KSDH (0.430 mg/L), which 

occurred in year 1 of the study (table 6). However, site KSDH 

had the second smallest number of samples collected at any of 

the study sites, so the water-quality conditions were not well 

characterized there, and most of the samples were collected 

early in the study period. Among all the sites, median TP 

concentrations were lowest at the end member sites, and 

highest at Tule Lake site LREW and KDD site KSDH, with 

median concentrations of 0.407 and 0.430 mg/L, respectively. 

The two highest maximum TP values were 0.950 mg/L at site 

KSDH, and 0.776 mg/L at site LREW. The lowest minimum 

TP value was 0.025 mg/L at site FMT, one of the end member 

sites. The median TP concentrations at canal sites within the 

KDD site group typically were higher than the upper basin 

and end member sites, with the exception of site LRBM. 

Concentrations of TP at site LRDC when water was flowing 

onto the project were slightly lower than concentrations when 

water was flowing towards the Klamath River (0.149 versus 

0.171 mg/L, respectively), although concentrations for the two 

flow directions were not statistically different when evaluated 

with a Mann-Whitney U test (p<0.05). Within the upper Lost 

River Basin sites, site LRBM had the highest median TP 

concentration of 0.183 mg/L, and site MCRV had the highest 

maximum TP concentration of 0.573 mg/L. 

TN values followed a similar pattern, except that median 

concentrations were lowest in the upper Lost River Basin 

sites, and second to lowest in the end member sites. Median 

TN concentration was highest at site PPD (4.08 mg/L), and 

lowest at site MCRV (0.764 mg/L), which suggests that the 

upper Lost River Basin might not be a significant source of 

TN compared to areas within the project near Tule Lake. For 

site LRDC, TN concentrations were statistically similar for 

both flow directions (table 6).

At the end member sites, TP concentrations were 

statistically higher at site KRK than at site FMT when 

combining data from all three study years, and TN 

concentrations were not statistically different (table 6). 

Median TP and TN concentrations were higher at site KRK 

than at site FMT during irrigation season, and similar at 

the two sites during non-irrigation periods (fig. 5). Median 

concentrations of TN and TP at the upper basin sites in years 1 

and 2 were variable at sites LRBH and LRBM, but site MCRV 

showed a smaller range of values in those years, particularly 

during irrigation seasons in years 1 and 2, suggesting that 

Gerber Reservoir does not contribute high concentrations of 

nutrients to the Lost River during irrigation season (fig. 6). 

In year 3, median concentrations of TN and TP were higher 

at site MCRV than at the other sites during the non-irrigation 

season (fig. 6). Water-quality samples at the Tule Lake sites 

were not collected in year 1, so only 2 years of data are 

available for analysis. More samples were collected at site 

LREW than site PPD because of lack of streamflow at site 

PPD (fig. 7). Because of the limited data at site PPD, more 

samples would provide for a more robust comparison if future 

studies are undertaken. Within the KDD group, site KSDH, 

which represents water moving from the Lower Klamath 

Wildlife Refuge into the Klamath Straits Drain, had higher 

concentrations of TP than the other sites during year 1 of 

the study and the irrigation season of year 2, and similar 

concentrations in non-irrigation year 2 (samples were not 

collected at site KSDH in year 3 because the canal was not 

flowing on sample collection days) (fig. 8). Concentrations 

of TP were statistically higher (p<0.05) at site KSDH when 

compared to the rest of the KDD sites after combining data 

from all 3 years (table 6), although these results are based 

on much fewer samples collected at site KSDH compared 

to the rest of the sites. The site with the second-highest 

concentrations of TP and TN in years 1 and 2 was site KSD97, 

which represents drainage water from irrigated lands in the 

KDD before entering the Klamath River. In year 3 of the 

study, site KSD97 had the highest median concentrations 

of TN and TP in both irrigation and non-irrigation seasons 

(fig. 8), and concentrations were statistically higher at that 

site for all three study years compared to canal sites NC and 

ADC97, which bring water from the Klamath River into the 

KDD for irrigation (table 6). 
Results 17

Table 6. Summary statistics of total and dissolved nutrient sample results, Klamath River and Lost River Basins, south-central Oregon 

and northern California, March 2012–March 2015.

[Site names and descriptions are shown in table 1; site locations are shown in figure 1. Site name abbreviation: LRDC (+) indicates samples that were collected 

when the flow direction was towards the Lost River; LRDC (-) indicates samples that were collected when the flow direction was toward the Klamath River. 

MWU (Mann-Whitney U statistical test): Sites that share a letter under the MWU column have sample concentrations that are the same statistically. Sites that 

do not share a letter have sample concentrations that are statistically different. Abbreviations: n, number of samples; N, nitrogen; mg/L, milligram per liter; ND, 

no data; <, less than]

Site name abbreviation

Total phosphorus (mg/L) Total nitrogen (mg/L) Orthophosphate (mg/L)

n Median Maximum 

Minimum MWU n Median Maximum 

Minimum MWU n Median Maximum 

Minimum MWU

Upper Lost River Basin

LRBM 46 0.183 0.469 0.028 a 46 0.874 2.56 0.413 a 46 <0.050 0.227 0.011 b

MCRV 51 0.093 0.573 0.053 a 51 0.764 6.27 0.349 a 51 0.031 0.136 0.011 c

LRBH 71 0.130 0.384 0.035 a 71 0.787 3.02 0.250 a 71 0.096 0.322 0.039 a

Tule Lake sites

LREW 40 0.407 0.776 0.207 ND 40 1.77 3.37 0.758 ND 40 0.274 0.602 0.146 ND

PPD 4 0.306 0.372 0.174 ND 4 4.08 5.08 3.52 ND 4 0.009 0.010 0.007 ND

Klamath Drainage District sites

KSDH 11 0.430 0.950 0.232 c 11 3.26 4.13 2.65 c 11 0.196 0.723 0.018 b,c

ADC97 54 0.160 0.370 0.078 a 54 1.46 3.85 0.754 a 54 0.063 0.245 0.010 a

NC 66 0.131 0.620 0.074 a 66 1.31 3.69 0.686 a,d 66 0.063 0.526 0.014 a

LRDC (+) 36 0.149 0.445 0.074 a 36 1.32 4.35 0.517 a,d 36 0.064 0.271 0.025 a,c

LRDC (-) 43 0.171 0.48 0.096 a 43 1.22 3.15 0.479 d 43 0.095 0.301 0.008 c

KSD97 52 0.320 0.545 0.121 b 52 2.73 5.02 1.36 b 52 0.151 0.390 0.008 b

End member sites

FMT 75 0.080 0.404 0.025 a 75 1.19 3.83 0.343 a 75 0.024 0.195 0.005 a

KRK 77 0.116 0.416 0.416 b 77 1.30 3.32 0.626 a 77 0.048 0.310 0.010 b

Site

Nitrate + nitrite as N (mg/L) Ammonia as N (mg/L)

n Median Maximum 

Minimum MWU n Median Maximum Minimum MWU

Upper Lost River Basin

LRBM 46 <0.050 0.271 <0.01 b 46 0.032 0.120 <0.01 a,b

MCRV 51 0.067 1.80 <0.01 c 51 0.019 0.100 <0.01 b

LRBH 71 0.296 2.19 <0.01 a 70 0.041 0.371 <0.01 a

Tule Lake sites

LREW 40 0.163 1.60 <0.01 ND 40 0.114 1.34 <0.01 ND

PPD 4 <0.010 0.024 <0.01 ND 4 0.022 0.338 0.02 ND

Klamath Drainage District sites

KSDH 11 <0.050 0.779 0.02 a,b,d 11 0.300 0.780 0.02 a,b

ADC97 54 0.108 0.580 <0.01 a,b 54 0.094 0.990 <0.00 a

NC 66 0.063 0.530 <0.01 a,d 66 0.101 1.46 0.01 a

LRDC (+) 36 <0.050 0.461 <0.01 d 36 <0.100 1.39 <0.01 a

LRDC (-) 43 0.246 1.56 <0.01 b,c 43 0.116 0.817 <0.01 a

KSD97 52 0.182 1.60 0.01 c 52 0.410 1.03 0.01 b

End member sites

FMT 75 0.136 0.469 <0.01 a 75 0.056 0.380 <0.01 a

KRK 77 0.117 0.670 <0.01 a 77 0.087 1.30 0.01 a
18 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

Table 7. Summary statistics of 5-day biochemical oxygen demand, 5-day carbonaceous biochemical oxygen demand, and 

chlorophyll-a sample results, Klamath River and Lost River Basins, south-central Oregon and northern California, March 2012–

March 2015.

[Site names and descriptions are shown in table 1; site locations are shown in figure 1. Site name abbreviation: LRDC (+) indicates samples that were collected 

when the flow direction was towards the Lost River; LRDC (-) indicates samples that were collected when the flow was toward the Klamath River. MWU 

(Mann-Whitney U statistical test): Sites that share a letter under the MWU column have sample concentrations that are the same statistically. Sites that do 

not share a letter have sample concentrations that are statistically different. Abbreviations: DOC, dissolved organic carbon; n, number of samples; TPC, total 

particulate carbon; TPN, total particulate nitrogen; μg/L, microgram per liter; mg/L, milligram per liter; ND, no data ; <, less than]

Site name 

abbreviation

BOD5 (mg/L) CBOD5 (mg/L) Chlorophyll-a (μg/L)

n Median Maximum 

Minimum MWU n Median Maximum Minimum MWU n Median Maximum Minimum MWU

Upper Lost River Basin

LRBM 46 <2.00 5.10 0.970 a 46 0.874 2.56 0.413 a 32 2.70 2.70 2.70 a

MCRV 50 1.42 7.50 0.490 b 51 0.764 6.27 0.349 a 50 5.00 28.0 1.00 a

LRBH 68 <2.00 4.41 0.650 a 71 0.787 3.02 0.250 a 55 4.50 25.4 2.80 a

Tule Lake sites

LREW 39 3.76 17.2 1.02 ND 38 3.00 17.1 0.680 ND 39 11.0 161 3.20 ND

PPD 4 12.2 17.7 5.61 ND 4 11.0 17.0 4.78 ND 4 99.2 150 27.3 ND

Klamath Drainage District sites

KSDH 9 6.60 12.0 2.90 a 9 4.70 9.00 2.20 a 12 51.7 167 4.20 a

ADC97 51 3.38 14.5 <2.00 a,b 50 2.62 12.0 1.50 a 54 22.4 115 7.30 a

NC 64 3.10 13.9 1.98 b 63 2.63 15.8 0.660 a 65 13.6 89.9 4.30 b,c

LRDC (+) 36 4.26 39.0 1.17 a,b 35 3.80 26.5 1.24 a 23 15.4 291 3.80 a,b,c

LRDC (-) 41 2.49 9.93 1.14 c 41 2.03 10.2 0.870 b 40 11.2 120 4.20 c

KSD97 50 4.47 13.2 1.63 a 49 3.35 15.3 1.28 a 52 22.2 174 4.20 a,b,c

End member sites

FMT 72 2.32 25.0 1.41 a 71 <2.00 23.9 0.600 a 59 11.2 330 4.10 a

KRK 74 2.70 10.2 1.07 a 73 2.10 7.54 0.910 a 77 16.0 69.2 3.50 a

Dissolved Nutrients

Over the course of the 3-year study, two different 

agencies collected samples and sent them to different 

laboratories, resulting in multiple MRLs for most of the 

constituents analyzed. The differences in MRLs are most 

noticeable in the dissolved nutrient results because nondetection was common for NO3+NO2 and NH3 results. The 

MDL for NO3+NO2 was 0.05 mg/L in year 1, and 0.01 mg/L 

in years 2 and 3. As a result, the median value at two sites, 

LRBM and KSDH, is reported as less than (<) 0.05 mg/L 

and, at site PPD, as <0.01 mg/L (table 6). The MRL for NH3

during year 1 changed once, from 0.10 to 0.03 mg/L, and then 

a second time for years 2–3 to 0.01 mg/L. As a result, median 

NH3 values at site LRDC(+) are reported as <0.10 mg/L 

in table 6. The MRL for ortho-P also changed from year 

1 (0.05 mg/L) to years 2 and 3 (0.004 mg/L), resulting in 

a median value reported as <0.05 mg/L at site LRBM and 

minimum value of 0.011 mg/L. All results with censored 

values are shown in table 8.

Table 8. Sample concentration results from all sites.

[Table 8 is a comma delimited file (.csv) and is available for download at 

https://doi.org/10.3133/sir20185075]

The highest median ortho-P concentration occurred at 

site LREW (0.274 mg/L), and the second-highest median 

concentration occurred at site KSDH (0.196 mg/L) (table 6). 

Concentrations of NO3+NO2 at all sites reported minimum 

concentrations that were less than the MRL of 0.01 mg/L, 

with the exception of sites KSDH and KSD97, which reported 

minimums of 0.0146 and 0.0108 mg/L, respectively, The 

highest median concentrations of NO3+NO2 occurred at 

site LRBH (0.296 mg/L) in the upper Lost River Basin and 

LRDC(-) (0.246 mg/L), when water was flowing from the 

project to the Klamath River. Overall, the lowest NO3+NO2

median concentrations occurred at sites LRBM, KSDH, 

and LRDC(+) (<0.05 mg/L), and PPD (<0.01 mg/L), with 

moderate concentrations at end member sites FMT and KRK, 

and sites ADC97 and KSD97. Median NH3 concentrations 

were highest at sites KSD97 (0.410 mg/L), with the next 

highest median concentration occurring at LRDC(-) 

(0.116 mg/L). The lowest median concentration occurred at 

site MCRV (0.0191 mg/L). Minimum NH3 concentrations at 

all sites were at or slightly above the MRL of 0.01 mg/L from 

the laboratory in study years 2 and 3. Site LRDC(+) reported 

median NH3 concentrations less than the MRL of 0.1 mg/L 

from study year 1.
Results 19 tac18-1203_fig 05

0

0.80.60.40.2

06420

0.60.40.2

0

2.52.01.51.00.5

0

1.61.20.80.4

Ammonia as N, in mg/L Nitrate + nitrite as N, in mg/L Orthophosphate, in mg/L Total nitrogen, in mg/L Total phosphorus, in mg/L

Year 1Irrigation season 

 Year 1Non-irrigation season

Year 2Irrigation season

Year 2Non-irrigation season

Year 3Irrigation season

Year 3Non-irrigation season

Notes: mg/L=milligrams per liter; numbers above boxes are n; and n value applies to all graphs by site except where noted.

Site

Value above 90th90th percentile75th percentileMedian25th percentile10th percentile

percentile

Value below 10th

percentile

EXPLANATION 

FMT KRK

14 14

FMT KRK

10 10

FMT KRK

12 12

FMT KRK

13 13

FMT KRK

13 14

FMT KRK

13 14

Figure 5.

Nutrient concentrations at end member sites, south-central Oregon, March 2012–March 2015. Site names and descriptions are shown in table 1; site locations 

are shown in figure 1.
20 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-1203_fig 06

0

0.80.60.40.2

06420

0.60.40.2

0

2.52.01.51.00.5

0

1.61.20.80.4

Year 1Irrigation season 

Ammonia as N, in mg/L Nitrate + nitrite as N, in mg/L Orthophosphate, in mg/L Total nitrogen, in mg/L Total phosphorus, in mg/L

 Year 1Non-irrigation season

Year 2Irrigation season

Year 2Non-irrigation season

Year 3Irrigation season

Year 3Non-irrigation season

11 11 11 14 12 10 7 11 14 6 10 5 5 16

1717

17

17

10 14

Notes: mg/L=milligrams 

per liter; numbers above boxes are n; and n value applies to all graphs by site except where noted.

LRBH LRBM MRCV LRBH LRBM LRBH LRBM MRCV LRBH LRBM MRCV LRBH LRBM MRCV LRBH MCRV

Site

Value above 90th90th percentile75th percentileMedian25th percentile10th percentile

percentile

Value below 10th

percentile

EXPLANATION 

Figure 6.

Nutrient concentrations at upper Lost River Basin sites, south-central Oregon, March 2012–March 2015. Site names and descriptions are shown in table 1; site 

locations are shown in figure 1.
Results 21 tac18-1203_fig 07

0

0.80.60.40.2

06420

0.60.40.2

0

2.52.01.51.00.5

0

1.61.20.80.4

Ammonia as N, in mg/L Nitrate + nitrite as N, in mg/L Orthophosphate, in mg/L Total nitrogen, in mg/L Total phosphorus, in mg/L

Site

No dataNo dataNo dataNo dataNo data

No dataNo dataNo dataNo dataNo data

LREW PPD LREW PPD LREW PPD LREW PPD

8 1 6 1 14 1 12 1

Year 1Irrigation season 

 Year 1Non-irrigation season

Year 2Irrigation season

Year 2Non-irrigation season

Year 3Irrigation season

Year 3Non-irrigation season

Notes: mg/L=milligrams per liter; numbers above boxes are n; and n value applies to all graphs by site except where noted.

Value above 90th90th percentile75th percentileMedian25th percentile10th percentile

percentile

Value below 10th

percentile

EXPLANATION 

Figure 7.

Nutrient concentrations at Tule Lake sites, northern California, March 2012–March 2015. Site names and descriptions are shown in table 1; site locations are 

shown in figure 1.
22 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-1203_fig 08

0

0.80.60.40.2

06420

0.60.40.2

0

2.52.01.51.00.5

0

1.61.20.80.4

14 14 2 16 13 10 4 4 10 7

Ammonia as N, in mg/L Nitrate + nitrite as N, in mg/L Orthophosphate, in mg/L

NC

ADC97

KSD97

KSDH

LRDC

NC

ADC97

KSD97

KSDH

LRDC

NC

ADC97

KSD97

KSDH

LRDC

NC

ADC97

KSD97

KSDH

LRDC

NC

ADC97

KSD97

LRDC

NC

ADC97

KSD97

LRDC

Total nitrogen, in mg/L Total phosphorus, in mg/L

12 7 3 12 11 9 5 2 13 11 6 7 14 13 2 14 14 11

Year 1Irrigation season 

 Year 1Non-irrigation season

Year 2Irrigation season

Year 2Non-irrigation season

Year 3Irrigation season

Year 3Non-irrigation season

Notes: mg/L=milligrams per liter; numbers above boxes are n; and n value applies to all graphs by site except where noted.

Value above 90th90th percentile75th percentileMedian25th percentile10th percentile

percentile

Value below 10th

percentile

EXPLANATION 

Figure 8.

Nutrient concentrations at Klamath Drainage District sites, south-central Oregon, March 2012–March 2015. Site names and descriptions are shown in table 1; site 

locations are shown in figure 1.
Results 23

At the end member sites, ortho-P concentrations were 

statistically higher at site KRK than at site FMT for all 

three years of the study, and NO3+NO2 and NH3 were not 

statistically different (table 6). During irrigation seasons, 

ortho-P and NH3 concentrations had a wider range of values, 

higher median concentrations, and higher peak concentrations 

at site KRK compared to site FMT (fig. 5). Among the upper 

Lost River Basin sites, median ortho-P concentrations were 

highest at site LRBH in both irrigation and non-irrigation 

seasons, with the exception of non-irrigation year 3 (fig. 6). 

Median NH3 concentrations were similar at the upper Lost 

River Basin sites for all 3 years regardless of irrigation season, 

and maximum values of NH3 at site LRBH were highest in 

year 3 (fig. 6).

Concentrations of dissolved nutrients at site LREW were 

of similar ranges regardless of irrigation or non-irrigation 

season (fig. 7). Median ortho-P concentrations at the KDD 

sites followed patterns similar to patterns for TP, with sites 

KSDH and KSD97 having the highest concentrations in 

years 2 and 3, and site KSD97 having the highest median 

concentration in year three. Overall, site KSD97 had the 

highest median ortho-P concentrations during the irrigation 

seasons among the KDD sites (fig. 8). NO3+NO2 median 

concentrations typically were elevated at the KDD sites during 

non-irrigation seasons, and NH3 median concentrations varied 

at all KDD sites in both irrigation and non-irrigation seasons 

(fig. 8).

Five-Day Biochemical Oxygen Demand (BOD5), 

5-Day Carbonaceous Biochemical Oxygen 

Demand (CBOD5), and Chlorophyll-a

Because of the change in analyzing laboratories between 

years 1 and 2 of the study, MRLs for BOD5 and CBOD5 were 

different for year 1 and years 2 and 3 of the project. The MRL 

in year 1 was 2.00 mg/L, and 0.300 mg/L for years 2 and 3. As 

a result, median values for these constituents are reported as 

less than the year-1 MRL of 2.00 mg/L for some of the study 

sites (table 7).

Median concentrations of BOD5 and CBOD5 were lowest 

among the upper Lost River Basin sites and highest at site 

PPD (12.2 and 11.0 mg/L, respectively, albeit this comparison 

is based on only four samples collected at site PPD over the 

3-year study period), and elevated at sites KSDH (6.60 and 

4.70 mg/L, respectively) and KSD97 (4.47 and 3.35 mg/L, 

respectively). The highest maximum BOD5 and CBOD5

concentrations were reported at sites LRDC(+) (39.0 and 

26.5 mg/L, respectively) and FMT (25.0 and 23.9 mg/L, 

respectively; table 7), likely representing the seasonal AFA 

blooms in Upper Klamath Lake. Median concentrations of 

chlorophyll-a were lowest at the upper Lost River Basin sites, 

moderate at sites FMT, KRK, LREW, LRDC, and NC, and 

elevated at sites KSDH and KSD97. The median concentration 

of chlorophyll-a was highest at site PPD (99.2 μg/L), and the 

maximum concentration of chlorophyll-a was highest at site 

FMT (330 μg/L).

At the end member sites, BOD5 and CBOD5

concentrations were not statistically different when data 

from all 3 years were evaluated with the Mann-Whitney 

U test. However, site FMT showed a wider range of values 

with higher maximum concentrations than site KRK during 

irrigation seasons (fig. 9), likely due to the content of AFA 

present in the samples during the summer algal bloom as 

represented by the elevated chlorophyll-a concentrations. The 

relation of chlorophyll-a and BOD5/CBOD5 concentrations 

has been shown by Sullivan and others (2010) in the Klamath 

River downstream of site FMT, and might suggest that 

chlorophyll-a is a predictor of BOD5/CBOD5 at some of the 

study sites. At the upper Lost River Basin sites, BOD5 and 

CBOD5 median concentrations were low compared to all the 

study sites, with multiple concentrations less than the MRL of 

2.0 mg/L (fig. 10, table 7). Concentrations of BOD5, CBOD5, 

and chlorophyll-a were similar at all three upper Lost River 

Basin sites regardless of irrigation or non-irrigation season 

(fig. 10).

At site LREW, BOD5 and CBOD5 concentrations were 

similar regardless of irrigation or non-irrigation season, and 

chlorophyll-a concentrations had a higher range of values 

and higher maximum concentrations in non-irrigation 

seasons compared to irrigation seasons (fig. 11). Among 

the KDD sites, BOD5, CBOD5, and chlorophyll-a median 

concentrations varied at all sites, and site LRDC showed the 

widest range of values and highest maximum concentrations 

during the irrigations seasons, although concentrations for all 

three constituents were not statistically different at most of the 

sites when combining results from all 3 years (fig. 12, table 7).

Dissolved Organic Carbon, Total Particulate 

Carbon, and Total Particulate Nitrogen 

The highest median concentration of DOC occurred at 

site KSDH in year 2 of the study (28.5 mg/L), when only two 

samples were collected. The second highest median DOC 

concentration was at site PPD (21.9 mg/L), also a site in which 

only two samples were collected. The highest maximum 

concentration among all sites also was collected at site KSDH 

(36.7 mg/L), the second highest maximum concentration was 

at site KSD97 (22.7 mg/L), followed by site PPD (22.0 mg/L). 

TPC and TPN median concentrations were highest at site 

PPD (10.9 and 1.77 mg/L, respectively), again with only two 

samples collected when the site was flowing (table 9).
24 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-1203_fig 09

Site

 03025201510

 5 0

3025201510

 5 0

 50

300250200150100

Five-day biochemical oxygen 

demand, in mg/L

Five-day carbonaceous biochemical 

 in ug/L a, Chlorophyll- oxygen demand, in mg/L

FMT KRK FMT KRK FMT KRK FMT KRK FMT KRK FMT KRK

14 1414 14

0 14

10 10

10 10

9 11

12 1211 1112 12

11 1111 1113 13

13 1413 1412 13

12 1312 1313 14

Year 1Irrigation season 

 Year 1Non-irrigation season

Year 2Irrigation season

Year 2Non-irrigation season

Year 3Irrigation season

Year 3Non-irrigation season

Notes: mg/L=milligrams per liter; numbers above boxes are n; and n value applies to all graphs by site except where noted.

Value above 90th90th percentile75th percentileMedian25th percentile10th percentile

percentile

Value below 10th

percentile

EXPLANATION 

Figure 9. Five-day biochemical oxygen demand, 5-day carbonaceous biochemical oxygen demand, and chlorophyll-a sample results at end member sites, south-central Oregon, March 2012–March 2015. Site names and descriptions are shown in table 1; site locations are shown in figure 1.
Results 25 tac18-1203_fig 10

Site

 03025201510

 5 0

3025201510

 5 0

 50

300250200150100

 in ug/L a, ChlorophyllYear 1 Irrigation season Year 1 Non-irrigation season Year 2 Irrigation season Year 2 Non-irrigation season Year 3 Irrigation season Year 3 Non-irrigation season

Notes: mg/L=milligrams per liter; numbers above boxes are n; and n value applies to all graphs by site except where noted.

Five-day carbonaceous biochemical 

oxygen demand, in mg/L

Five-day biochemical oxygen 

demand, in mg/L

LRBH LRBM MCRV

11 11 1111 11 11

0 0 11

LRBH LRBM

14 1214 1210 9

LRBH LRBM MCRV

10 7 1196 1010 7 11

LRBH LRBM

11 6 911 6 914 6 10

LRBH

5

55

5

4 4

LRBH LRBM MCRV MCRV MCRV

17 10 14

17 10 14

17 10 14

Value above 90th90th percentile75th percentileMedian25th percentile10th percentile

percentile

Value below 10th

percentile

EXPLANATION 

Figure 10. Five-day biochemical oxygen demand, 5-day carbonaceous biochemical oxygen demand, and chlorophyll-a sample results at upper Lost River Basin sites, south-central Oregon, March 2012–March 2015. Site names and descriptions are shown in table 1; site locations are shown in figure 1.
26 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-1203_fig 11

Site

 03025201510

 5 0

3025201510

 5 0

 50

300250200150100

 in ug/L a, Chlorophyll7 1

8 1

LREW PPD

8 1

LREW PPD

6 1

LREW PPD

13 1

12 112 1

LREW PPD

12 1

5 1 14 1

14 1 15

No dataNo dataNo data

No dataNo dataNo data

Year 1Irrigation season 

 Year 1Non-irrigation season

Year 2Irrigation season

Year 2Non-irrigation season

Year 3Irrigation season

Year 3Non-irrigation season

Notes: mg/L=milligrams per liter; numbers above boxes are n; and n value applies to all graphs by site except where noted.

Five-day carbonaceous biochemical 

oxygen demand, in mg/L

Five-day biochemical oxygen 

demand, in mg/L

Value above 90th90th percentile75th percentileMedian25th percentile10th percentile

percentile

Value below 10th

percentile

EXPLANATION 

Figure 11. Five-day biochemical oxygen demand, 5-day carbonaceous biochemical oxygen demand, and chlorophyll-a sample results at Tule Lake sites, northern 

California, March 2012–March 2015. Site names and descriptions are shown in table 1; site locations are shown in figure 1.
Results 27 tac18-1203_fig 12

Site

 5 0

3025201510

 5 0

 03025201510

300250200150100

 50

 in ug/L a, ChlorophyllNC

ADC97

KSD97

KSDH

LRDC

NC

ADC97

KSD97

KSDH

LRDC

NC

ADC97

KSD97

KSDH

LRDC

NC

ADC97

KSD97

KSDH

LRDC

NC

ADC97

KSD97

LRDC

NC

ADC97

KSD97

LRDC

14 14 2 2 1314 14 2 16 1314 14 2 16 13

11 5 5 9 7

10 4 4 10 710 4 4 10 7

12 7 3 12 11

10 6 3 11 10

11 7 3 12 11

9 5 2 13 117 3 0 11 107 3 0 11 10

5 6 13 126 7 14 136 7 14 13

2 14 11 11

2 14 14 10

2 14 14 10

Year 1Irrigation season 

 Year 1Non-irrigation season

Year 2Irrigation season

Year 2Non-irrigation season

Year 3Irrigation season

Year 3Non-irrigation season

Notes: mg/L=milligrams per liter; numbers above boxes are n; and n value applies to all graphs by site except where noted.

Five-day carbonaceous biochemical 

oxygen demand, in mg/L

Five-day biochemical oxygen 

demand, in mg/L

Value above 90th90th percentile75th percentileMedian25th percentile10th percentile

percentile

Value below 10th

percentile

EXPLANATION 

Figure 12. Five-day biochemical oxygen demand, 5-day carbonaceous biochemical oxygen demand, and chlorophyll-a sample results at Klamath Drainage District sites, 

south-central Oregon, March 2012–March 2015. Site names and descriptions are shown in table 1; site locations are shown in figure 1.
28 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

Table 9. Summary statistics of dissolved organic carbon, total particulate carbon, and total particulate nitrogen 

sample results, Klamath River and Lost River Basins, south-central Oregon and northern California, March 2012–

March 2015.

[Site names and descriptions are shown in table 1; site locations are shown in figure 1. Site name abbreviation: LRDC (+) indicates 

samples that were collected when the flow direction was towards the Lost River; LRDC (-) indicates samples that were collected when 

the flow direction was toward the Klamath River. Abbreviations: DOC, dissolved organic carbon; n, number of samples; TPC, total 

particulate carbon; TPN, total particulate nitrogen; μg/L, microgram per liter; mg/L, milligram per liter; ND, no data ; <, less than]

Site name abbreviation

DOC (mg/L) TPC (mg/L) TPN (ug/L)

n Median Maximum 

Minimum n Median Maximum 

Minimum n Median Maximum 

Minimum

Upper Lost River Basin

LRBM 7 9.20 11.3 5.83 7 1.24 10.8 0.506 7 0.155 1.39 0.082

MCRV 11 5.84 8.64 4.96 11 0.915 8.40 0.463 11 0.122 1.36 <0.030

LRBH 12 6.63 9.45 1.61 12 0.665 2.61 0.368 12 0.074 0.418 <0.030

Tule Lake sites

LREW 9 6.32 9.71 4.61 9 1.81 10.7 0.351 9 0.288 1.85 0.067

PPD 2 21.9 22.0 21.8 2 10.9 12.7 9.24 2 1.77 2.04 1.50

KDD sites

KSDH 2 28.5 36.7 20.4 2 2.61 3.95 1.27 2 0.360 0.541 0.178

ADC97 9 6.45 9.24 4.06 9 2.15 4.13 1.75 9 0.357 0.830 0.278

NC 11 5.49 7.58 4.15 11 1.66 5.97 0.923 11 0.274 0.919 0.147

LRDC (+) 6 5.20 7.25 4.33 6 2.7 5.84 0.687 6 0.458 1.26 0.084

LRDC (-) 7 4.66 6.69 2.73 7 1.35 3.10 0.673 7 0.235 0.624 0.087

KSD97 10 18.3 22.7 9.09 10 2.11 8.10 0.901 10 0.315 1.10 0.114

End member sites

FMT 11 4.11 6.45 3.00 11 1.79 8.22 1.10 11 0.308 1.59 0.063

KRK 13 6.12 8.67 3.98 13 1.68 6.08 1.03 13 0.255 1.11 0.125

DOC concentrations were highest overall at site KSDH 

when it was sampled, and also were elevated at sites PPD 

and KSD97. Sites PPD and KSD97 also showed the highest 

median TPC concentrations. Median DOC concentrations 

at sites other than sites KSDH and KSD97 were much 

lower, with concentrations less than 10 mg/L. Median DOC 

concentrations increased from site LREW(6.32 mg/L) 

upstream of Tule Lake to site PPD (21.9 mg/L) and then 

to site KSDH (28.5 mg/L), but were lower at site KSD97 

(18.3 mg/L). TPC did not follow this trend, in that TPC 

concentrations increased from sites LREW (1.81 mg/L) to 

PPD (10.9 mg/L), again resulting in increased concentrations 

from Tule Lake, but were lower at site KSDH (2.61 mg/L), 

and lower still at site KSD97 (2.11 mg/L) (table 9). However, 

with only two samples collected at sites PPD and KSDH 

over the 3-year study period, compared to 10 samples 

collected at KSD97, these relations are not well defined by 

the available data. Additionally, during the dry years of this 

study, the flowpath from sites LREW to KSD97 was largely 

discontinuous, and sample concentrations at site KSD97 were 

more influenced by Ady and North Canals than site KSDH 

during those years.

The median TPN concentration was highest at site PPD, 

based on two samples, and the median TPN concentration 

was lowest at site LRBH in the upper Lost River Basin. The 

second highest concentration occurred at site LRDC(+) when 

water was flowing from the Klamath River to the Reclamation 

project. Overall, median TPN concentrations were highest 

at site PPD, and sites within the KDD that divert water from 

the Klamath River, as well as at site FMT (which represents 

Klamath Lake water). The concentrations were lowest in the 

upper Lost River Basin at sites LRBM, MCRV, and LRBH 

(table 9).

Load Estimates

TP, TN, BOD5, and CBOD5 loads are presented in 

tables for each site during the irrigation and non-irrigation 

seasons for the 3 years of the study. Loads at two of the sites 

(sites FMT and KRK) were computed using the LOADEST 

model. All other sites are reported as the average of computed 

instantaneous loads during the irrigation or non-irrigation 

seasons.
Results 29

Klamath River at Keno (Site KRK) LOADEST 

Model Results

As explained in the section, “Methods,” multivariate and 

seasonal wave regression models were evaluated to compute 

loads of TP, TN, BOD5, and CBOD5. Seasonal wave models 

best described loads of TN and TP, and a four-parameter 

regression model best described loads of BOD5 and CBOD5

(table 10). For TN and TP, the seasonal wave models were 

a better fit because the regulated flows downstream of 

Keno Dam had little effect on the concentrations of those 

constituents. Instead, the data fluctuate seasonally, with 

concentration peaks occurring during the summer (fig. 13). 

A time series of computed daily TP and TN loads using 

the seasonal wave, plus 95-percent prediction intervals, is 

shown in figure 14. Daily TP loads modeled (computed) 

with LOADEST ranged from 50 to 930 kg/d for the 3 years 

of the study. The minimum instantaneous TP load used in 

the calibration dataset was 48 kg/d, and the maximum load 

was 856 kg/d. Daily TN loads computed with LOADEST 

ranged from 730 to 8,711 kg/d for the three study years. 

The minimum instantaneous TN load used in the calibration 

dataset was 625 kg/d, and the maximum was 7,000 kg/d. 

Statistics and model summaries for rejected models are shown 

in appendix 1.

The LOADEST-selected best fit model for BOD5 was 

a four parameter model with components of streamflow 

and seasonality as explanatory variables (table 10). The 

LOADEST-selected best fit CBOD5 model was a five 

parameter model with components of streamflow, seasonality, 

and decimal time. The next-lowest AIC-scored model for 

CBOD5 was the four parameter model, an identical model 

form to the best-fit BOD5 model. The model results of the 

four and five parameter CBOD model showed a similar R2

between the two models, and similar bias percentages, but the 

five-parameter model included two non-significant (p>0.05) 

explanatory variables compared to one non-significant 

explanatory variable for the four-parameter model. 

0.10

0.20

0.02

0.30

0.03

0.50

0.05

0.07

0.10

0.20

0.30

0.40

0.50

0.06

0.07

0.08

0.10

0.20

0.30

0.40

0.06

0.07

0.08

0.09

0.10

0.20

0.30

0.03

0.40

0.04

0.60

0.06

0.08

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

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

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

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

Total phosphorus, in milligrams per liter Total phosphorus, in milligrams per liter

Total nitrogen, in milligrams per liter Total nitrogen, in milligrams per liter

A B

C D

Figure 13. Seasonal peak concentrations of (A) total phosphorus at site FMT, (B) total nitrogen at 

site FMT, (C) total phosphorus at site KRK, and (D) total nitrogen at site KRK, south-central Oregon, 

March 2012–March 2015. Site names and descriptions are shown in table 1; site locations are shown 

in figure 1.
30 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015 Table 10. Model statistics for LOADEST results at Klamath River at sites KRK and FMT, south-central Oregon. [Site names and descriptions are shown in table 1; site locations are shown in figure 1. Abbreviations: 5-day BOD5, biochemical oxygen demand; 5-day CBOD5, carbonaceous biochemical oxygen demand; dtime, decimal time; ln, natural logarithm; PPCC, probability plot correlation coefficient; Q, streamflow; TN, total nitrogen; TP, total phosphorus; >, greater than; < less than] Constituent Model type Number of observations in calibration dataset Number of uncensored observations in calibration dataset Model equation Coefficient of determination (R2) PPCC Load bias percentage (Bp) Klamath River at Keno (site KRK) TP Seasonal wave 72 72 ln(TP) = 5.9 + 1.06center(ln(Q)) + 1.10seasonalWave(dtime,0.60,3,1) 0.82 0.99 0.23 TN Seasonal wave 77 77 ln(TN) = 8.2 + 0.90center(ln(Q)) + 0.82seasonalWave(dtime,0.62,2,1) 0.76 0.99 0.15 BOD5 Four parameter 74 63 ln(BOD) = 8.60 + 0.59 ln(Q) + 0.084sin(2πdtime) – 0.45cos(2πdtime) 0.53 0.99 3.31 CBOD5 Four parameter 73 56 ln(CBOD) = 8.40 + 0.48ln(Q) + 0.081sin(2πdtime) – 0.45cos(2πdtime) 0.46 0.98 4.50 Fremont Bridge (site FMT) TP Seasonal wave 77 77 ln(TP) = 5.76 + 0.99center(ln(Q)) + 1.62(seasonalWave(dtime,0.57,2,1) 0.91 0.97 0.170 TN Seasonal wave 77 77 ln(TN) = 8.16 + 0.83center(ln(Q)) + 1.44(seasonalWave(dtime,0.50,1,4) 0.84 0.99 -1.95 BOD5 Seasonal wave 74 74 ln(BOD) = 9.286 + 0.815center(lnQ) – 1.943seasonalWave(dtime,0.34,9,1) 0.84 0.99 -11.01 CBOD5 Seasonal wave 73 73 ln(CBOD) = 9.17 + 0.785center(lnQ) – 2.06seasonalWave(dtime,0.35,9,1) 0.83 0.98 -13.1
Results 31 tac18-1203_fig 14

Upper and lower 95-percent prediction intervalObserved instantaneous TP load

EXPLANATION

Upper and lower 95-percent prediction intervalObserved instantaneous TN load

EXPLANATION

Computed daily TP load, in kilograms

Computed daily TN load, in kilograms

A J M F M J J A S O D N A J F M M J J A S O D N J F M A M M J J A S O D N

2012 2013 2014 2015

A.

B.

Daily total phosphorus (TP) load, in kilograms Daily total nitrogen (TN) load, in kilograms 500

2,0001,5001,000

00

5,000

15,00010,000

Figure 14. Time series of computed daily loads, associated 95-percent prediction intervals, and observed instantaneous loads of total phosphorus (A), and total nitrogen (B) at site KRK, south-central Oregon, March 2012–March 2015. Site name and description are shown in table 1; site location is shown in figure 1.
32 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

Because model statistics were similar between the two models, 

the four-parameter model was selected to compute loads to 

reduce bias in the load predictions by reducing the number 

of non-significant explanatory variables. A time series of 

computed daily BOD5 and CBOD5 loads plus 95-percent 

prediction intervals is shown in figure 15. A number of the 

BOD5 and CBOD5 analytical results were reported as “less 

than” the reporting limit of the analyzing laboratory, so 

the LOADEST models for these two parameters contained 

censored values in the calibration dataset. Coefficients of 

determination were lower for BOD5 (R2=0.53) and CBOD5

(R2=0.46) than the seasonal wave models for TP and TN, but 

load bias percentages (Bp) were still less than 5 percent for 

both models (table 10).

Comparison of modeled daily loads from LOADEST 

and measured loads from instantaneous discrete samples 

and streamflow shows better agreement for the TP and 

TN models compared to the BOD5 and CBOD5 models at 

site KRK (fig. 16). The BOD5 and CBOD5 models tend to 

have the highest percent difference when the models were 

underestimating the measured loads in July and August, 

and when the models were overestimating the loads in May 

and June. This trend suggests that the LOADEST model 

does not accurately characterize the peak loads of BOD5

and CBOD5 in mid-to-late summer when the AFA biomass 

is reaching seasonal peak levels in the Klamath River, and 

that the parameters available in the model are not adequately 

describing a process that causes the peak loads to occur.

Fremont Bridge (site FMT) LOADEST 

Model Results

The model-selection process at site FMT followed the 

same process used at site KRK. TP and TN concentrations 

showed strong seasonal patterns (fig. 13), and, thus, seasonal 

wave models were selected for both of these constituents 

(table 10). The strong seasonal patterns for TP and TN at this 

site on the south end of Upper Klamath Lake likely represent 

the summer peak concentrations of these constituents, which 

are coincident with the persistent algal bloom in the lake. 

A time series of computed daily TP and TN loads using the 

seasonal wave, plus 95-percent prediction intervals, is shown 

in figure 17. Daily TP loads computed with LOADEST 

ranged from 32 to 1,872 kg/d for the 3 years of the study. 

The minimum instantaneous TP load used in the calibration 

data set was 33 kg/d, and the maximum was 1707 kg/d. 

Daily TN loads computed with LOADEST ranged from 

570 to 16,467 kg/d for the three study years. The minimum 

instantaneous TN load used in the calibration data set was 

672, and the maximum load was 16,431. Statistics and model 

summaries for rejected models are shown in appendix 1.

BOD5 and CBOD5 loads at site FMT initially were best 

described by a four-parameter model with streamflow and 

seasonality terms as explanatory variables. After the modeled 

daily loads, prediction intervals, and measured instantaneous 

loads were plotted, these models were shown to underestimate 

the measured instantaneous loads. Seasonal wave models 

better explained the measured loads for both BOD5 and 

CBOD5, although uncertainty around both of these estimates 

was high, particularly during the summer when algal biomass 

is high in the lake (fig. 18). Coefficients of determination were 

slightly lower for BOD5 (R2=0.84) and CBOD5 (R2=0.83) 

(table 10) than for the seasonal wave models for TP and 

TN. Load bias percentages (Bp) were greater for BOD5

(-11.01 percent) and CBOD5 (-13.1 percent) compared to 

results at site KRK, where Bp values for both BOD5 and 

CBOD5 were less than 5 percent. 

Comparison of modeled loads from LOADEST and 

measured loads from instantaneous discrete samples and 

streamflow shows better agreement for the TP and TN models 

compared to the BOD5 and CBOD5 models at site FMT 

(fig. 19). As with site KRK, the BOD5 and CBOD5 models at 

site FMT tended to have the highest percent difference when 

the models were underestimating the measured loads, except 

that the models at site FMT resulted in underestimation in 

June and July. Model overestimation occurred in April and 

May at site FMT, compared to May and June at site KRK. This 

trend suggests that the LOADEST model does not accurately 

characterize the peak loads of BOD5 and CBOD5 in midto-late summer when the AFA biomass is reaching seasonal 

peak levels in Upper Klamath Lake, and that the parameters 

available in the model also are not adequately describing a 

process that causes the peak loads to occur at this site.

The computation of loads at sites KRK and FMT allows 

for direct comparison of the upper and lower boundaries for 

this study during irrigation and non-irrigation seasons. Loads 

at site FMT generally were higher than loads at site KRK 

during irrigation seasons for all constituents, and lower than 

loads at site KRK during non-irrigation seasons, but well 

within the 95-percent prediction intervals for those models 

(table 11). Most notable are the BOD5 and CBOD5 loads at 

site FMT, which were an order of magnitude higher than loads 

at site KRK during all irrigation seasons. Because irrigation 

season coincides with the seasonal algal blooms in Upper 

Klamath Lake, the large load values for BOD5 and CBOD5

likely represent the oxygen demand of AFA in the samples 

collected from site FMT. At both sites, constituent loads were 

higher during irrigation season compared to non-irrigation 

seasons, although the magnitude of differences was different 

depending on the constituent. 
Results 33 tac18-1203_fig 15

Computed daily BODUpper and lower 95-percent prediction interval

5 load, in kilograms

Observed instantaneous BOD5 load

EXPLANATION

Computed daily CBODUpper and lower 95-percent prediction interval

5 load, in kilograms

Observed instantaneous CBOD5 load

EXPLANATION

A J M F M J J A S O D N A J F M

M J J A S O D N J F M A M

M J J A S O D N

0

5,000

45,00040,00035,00030,00025,00020,00015,00010,000

0

5,000

45,00040,00035,00030,00025,00020,00015,00010,000

2012 2013 2014 2015

A.

B.

Five-day carbonaceous biochemical oxygen demand (CBOD5),

in kilograms per day

Five-day biochemical oxygen demand (BOD5),

in kilograms per day

Figure 15. Time series of computed daily loads, associated 95-percent prediction intervals, and observed instantaneous loads of 5-day biochemical oxygen demand (A), and 5-day carbonaceous biochemical oxygen demand (B) at site KRK, south-central Oregon, March 2012–March 2015. Site name and description are shown in table 1; site location are shown in figure 1.
34 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-1203_fig16

−150

−100

 −50

 0

 50

 100

−150

−100

 −50

 0

 50

 100

−150

−100

 −50

 0

 50

 100

−100

 −50

 0

 50

 100

Percent difference

A. Total phosphorus

B. Total nitrogen

C. Five-day biochemical oxygen demand

D. Five-day carbonaceous biochemical oxygen demand

AM M J J A S O DN J MF M J J A S O DN A J F M M J J A S O DN J F M A

2012 2013 2014 2015

Model over-estimation

Model under-estimation

Year 3

Figure 16. Percent difference between modeled (LOADEST) and measured loads for total phosphorus (A), total nitrogen (B), 

5-day biochemical oxygen demand (C), and 5-day carbonaceous biochemical oxygen demand at site KRK (D), south-central 

Oregon, March 2012–March 2015. Site name and description are shown in table 1; site location is shown in figure 1.

Instantaneous and Daily Load Averaging Results

Nutrient loads at the remaining study sites, not 

including sites FMT and KRK, were calculated by averaging 

instantaneous loads for irrigation and non-irrigation seasons 

as described in the section, “Methods.” The sites are evaluated 

based on their geographic location within the project by 

separating them into three distinct groups—(1) Upper Lost 

River Basin (sites LRBM, MCRV, and LRBH); (2) Tule Lake 

sites (LREW and PPD), and (3) Klamath Drainage District 

(KDD) sites (KSDH, ADC97, NC, LRDC, KSD97). The KDD 

sites were selected because they are either managed for water 

delivery within the KDD, or because irrigation and return 

flows from irrigation areas within KDD have the potential to 

affect water quality at a study site. Site LRDC was included 

in this group because of its spatial location and so it could 

be grouped with the other canal sites, but site LRDC does 

not supply water to the KDD. Water flowing in site LRDC is 

delivered either to the Tulelake Irrigation District lands, or 

the Klamath Irrigation District lands. Loads at site LRDC are 

represented as either negative (flowing to the Klamath River) 

or positive (flowing towards the Lost River), consistent with 

the flow direction data reported at the streamgage.
Results 35 tac18-1203_fig 17

A J M F M J J A S O D N A J F M M J J A S O D N J F M A M M J J A S O D N

2012 2013 2014 2015

A.

B.

Daily total phosphorus (TP) load, in kilograms Daily total nitrogen (TN) load, in kilograms 0 500

4,0003,5003,0002,5002,0001,5001,000

0

5,000

30,00025,00020,00015,00010,000

Upper and lower 95-percent prediction intervalObserved instantaneous TP load

EXPLANATION

Computed daily TN load, in kilogramsUpper and lower 95-percent prediction intervalObserved instantaneous TN load

EXPLANATION

Computed daily TP load, in kilograms

Figure 17. Time series of computed daily loads, associated 95-percent prediction intervals, and observed instantaneous loads of total phosphorus (A), and total nitrogen (B) at site FMT, south-central Oregon, March 2012–March 2015. Site name and description are shown in table 1; site location is shown in figure 1.
36 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-1203_fig 18

A J MF M J J A S O DN A J F M M J J A S O DN J F M AM M J J A S O DN

2012 2013 2014 2015

A.

B.

Five-day biochemical oxygen demand (BOD5) load,

in kilograms per day

Five-day carbonaceous biochemical oxygen demand (CBOD5) load,

in kilograms per day

0

50,000

200,000150,000100,000

0

50,000

200,000150,000100,000

Upper and lower 95-percent prediction intervalObserved instantaneous BOD5 load

EXPLANATION

Computed daily CBODUpper and lower 95-percent prediction interval 5 load, in kilograms

Observed instantaneous CBOD5 load

EXPLANATION

Computed daily BOD5 load, in kilograms

Figure 18. Time series of computed daily loads, associated 95-percent prediction intervals, and observed instantaneous loads of 5-day biochemical oxygen demand (A), 

and 5-day carbonaceous biochemical oxygen demand (B) at site FMT, south-central Oregon, March 2012–March 2015. Site name and description are shown in table 1; site location is shown in figure 1.
Results 37

tac18-1203_fig19

Percent difference

A. Total phosphorus

B. Total nitrogen

C. Five-day biochemical oxygen demand

D. Five-day carbonaceous biochemical oxygen demand

AM M J J A S O DN J MF M J J A S O DN A J F M M J J A S O DN J F M A

2012 2013 2014 2015

Model over-estimation

Model under-estimation

−150

−100

 −50

0

 50

 100

−150

−100

 −50

0

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 100

−150

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0

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−150

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 −50

0

 50

 100

5-day biochemical oxygen demand (C), and 5-day carbonaceous biochemical oxygen demand (D) at site FMT, March 2012–

March 2015, south-central Oregon. Site name and description are shown in table 1; site location is shown in figure 1.

Figure 19. Percent difference between modeled (LOADEST) and measured loads for total phosphorus (A), total nitrogen (B), 

Upper Lost River Basin Sites

Average loads of TP and TN were lower at site LRBM 

(the farthest upstream site in the study) during irrigation 

and non-irrigation seasons compared to sites MCRV and 

LRBH (table 12). TP and TN loads at site LRBM were lower 

during irrigation season compared to non-irrigation season 

for all three study years, which was atypical compared to 

other monitoring sites. No samples were collected during 

irrigation year 3 because of the lack of streamflow at that site, 

so loads are represented as zero. Average TP and TN loads 

at site LRBH were higher during the non-irrigation season 

compared to irrigation season. Streamflows are higher at that 

site during non-irrigation seasons because much of the water 

in Lost River is diverted upstream of the sampling location 

during irrigation season. Fewer samples were collected at all 

sites during irrigation season year 3 (summer 2014) owing 

to lack of water from the eastern side of the Reclamation 

project because of drought conditions. No samples were 

collected at site LRBM because of lack of streamflow, and 

only five samples were collected at sites MCRV and LRBH. 
38 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

Table 11. Average modeled (LOADEST) mean daily loads of total phosphorus, total 

nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous biochemical 

oxygen demand at sites FMT and KRK during irrigation and non-irrigation seasons, 

south-central Oregon, March 2012–March 2015. 

[Site names and descriptions are shown in table 1; site locations are shown in figure 1. 

Abbreviations: ft3/s, cubic foot per second; kg/d, kilogram per day]

Site name 

abbreviation

Total 

phosphorus 

(kg/d)

Total 

nitrogen 

(kg/d)

Biological oxygen demand 

(kg/d) Average 

streamflow 

(ft3 5-day /s) 5-day 

carbonaceous

Irrigation year 1 (201 days)

FMT 726 7,590 29,700 26,300 2,200

KRK 527 4,450 9,750 7,410 1,291

Non-irrigation year 1 (145 days)

FMT 111 1,870 3,700 3,150 655

KRK 172 2,060 3,670 3,040 678

Irrigation year 2 (189 days)

FMT 555 5,990 24,200 21,800 1,480

KRK 302 2,760 6,980 5,410 689

Non-irrigation year 2 (168 days)

FMT 120 1,950 3,990 3,390 715

KRK 188 2,220 4,270 3,470 739

Irrigation year 3 (195 days)

FMT 529 5,750 23,200 20,800 1,440

KRK 344 3,070 7,430 5,740 772

Non-irrigation year 3 (200 days)

FMT 110 1,780 3,690 3,150 653

KRK 176 2,100 4,110 3,350 695

In contrast to sites LRBM and LRBH, TP and TN loads at 

site MCRV were higher during irrigation season compared 

to non-irrigation season in years 2 and 3. Instantaneous loads 

at site MCRV during the non-irrigation period in year 1 

were calculated at zero because of zero flows reported by 

Reclamation for that time period. (Reclamation reported zero 

flow at site MCRV outside the irrigation seasons, and USGS 

did not begin streamflow measurements until year 2 of the 

study). Overall, TN and TP loads were highest at site MCRV 

for irrigation periods for all 3 years of the study, likely owing 

to higher streamflow during irrigation season at that site. 

BOD5 and CBOD5 loads were lowest at site LRBM 

during irrigation periods for years 1 and 2 (no data were 

collected in year 3), and BOD5 and CBOD5 loads were highest 

at site MCRV during irrigation periods for all 3 years, owing 

to the higher streamflows at that site (table 12). The converse 

relation occurred during non-irrigation periods for years 2 and 

3, when BOD5 and CBOD5 loads were lowest at site MCRV 

compared to the other two sites and highest at site LRBH. 

Overall, BOD5 and CBOD5 loads were highest at site LRBH 

for all non-irrigation periods.
Results 39

Table 12. Averaged instantaneous loads of total phosphorus, total nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous biochemical oxygen demand, during irrigation and non-irrigation seasons, at upper Lost River Basin sites LRBM, MCRV, and LRBH, Lost River and Klamath River Basins, southcentral Oregon, March 2012–March 2015.[Site names and descriptions are shown in table 1; site locations are shown in figure 1. Abbreviations: n, number of instantaneous loads used in the averaging calculation; sd, standard deviation; ft3/s, cubic foot per second; kg/d, kilogram per day]

Site name 

abbreviation

Total phosphorus (TP) Total nitrogen (TN) 5-day biochemical oxygen demand (BOD5) 5-day carbonaceous biochemical oxygen demand (CBOD5) Average streamflow 

(ft3/s) TP (kg/d) n sd TN (kg/d) n sd BOD5 (kg/d) n sd CBOD5 (kg/d) n sd

Irrigation year 1 (129 days LRBM, 147 days MCRV and LRBH) 

LRBM 1.69 9 0.657 6.13 9 2.33 13.8 9 5.53 13 9 4.64 2.63MCRV 24.8 11 10.6 210 11 72.8 771 11 636 540 11 180 110LRBH 24.6 11 19.2 86.2 11 66.9 225 11 143 225 11 143 45.9

Non-irrigation year 1 (236 days LRBM, 198 days MCRV and LRBH)

LRBM 3.55 16 7.4 22.8 16 44.2 50.3 16 92.4 49.7 16 92.4 9.89MCRV 0 13 0 0 13 0 0 13 0 0 13 0 0LRBH 38.6 14 53.3 273 14 329 501 14 413 484 14 386 98.2

Irrigation year 2 (106 days LRBM, 152 days MCRV and LRBH)

LRBM 0.076 8 0.107 0.317 8 0.442 1.12 7 1.43 0.924 6 1.56 0.132MCRV 20 11 2.97 144 11 33.5 317 11 127 253 10 131 95.3LRBH 5.97 11 6.63 31.2 11 54.8 76.6 11 88.6 68.5 10 87.5 13.8

Non-irrigation year 2 (259 days LRBM, 212 days MCRV and LRBH)

LRBM 0.704 14 0.863 3.69 14 3.76 10.7 12 8.63 10 12 8.42 1.46MCRV 0.252 11 0.118 2.07 11 0.908 3.89 10 2.49 3.46 10 2.22 1.16LRBH 18.2 14 25.1 129 14 134 303 11 439 262 11 355 70.7

Irrigation year 3 (0 days LRBM, 77 days MCRV and LRBH)

LRBM 0 4 0 0 4 0 0 4 0 0 4 0 0MCRV 27.8 5 6.68 181 5 14.8 309 5 30.8 229 5 42 94.6LRBH 2.37 5 2.24 7.95 5 8.73 53.5 5 87.5 44 5 75.9 5.86

Non-irrigation year 3 (288 days LRBM,MCRV, and LRBH)

LRBM 0.88 22 2.16 9.07 22 21.2 22.7 22 60 16.3 22 41.6 5.01MCRV 0.58 21 0.653 4.15 21 4.28 2.52 21 2.55 1.74 21 1.76 0.807LRBH 13.2 17 17.7 163 17 161 203 17 288 174 17 274 43.4
40 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

Tule Lake Sites

Sites LREW and PPD were added to the project in year 

2 of the study when USGS began collecting samples and 

streamflow measurements. Site PPD, which pumps water 

from Tule Lake west towards the Lower Klamath Wildlife 

Refuge, pumped water infrequently in years 2 and 3 of the 

study, because of ongoing drought conditions. As a result, only 

two samples were collected in each year, one during irrigation 

season and one during non-irrigation season, and all other 

loads were reported as zero when the site was not flowing 

and incorporated in the averages. As a result, more samples 

were collected at site LREW than at site PPD. (table 13). TP 

loads were similar at both sites in year 2, but were an order 

of magnitude higher at site LREW in year 3. TN loads were 

higher at site PPD compared to site LREW in all 3 years, with 

the exception of the non-irrigation period in year 3. BOD5 and 

CBOD5 loads were higher at site PPD compared to site LREW 

in year 2 than in year 3. Overall, loads of all constituents at 

the Tule Lake sites were higher during irrigation and nonirrigation periods than at the upper Lost River Basin sites, 

which is likely a function of the higher concentrations at sites 

LREW and PPD rather than differences in streamflow between 

these two project groups. 

Klamath Drainage District Sites and Site LRDC

Site KSDH is located at the headworks of the Klamath 

Straits Drain, which is the outlet of the Lower Klamath 

Wildlife Refuge. During the study period, water rarely 

flowed from the refuge into the canal, resulting in very few 

instantaneous load calculations. Only two samples during 

years 2 and 3 of the study were collected when water was 

flowing. All other loads were reported as zero when the site 

was not flowing and were used in the calculations of average 

loads. Samples were collected by Reclamation during year 1 

of the study when the canal was flowing, but streamflow could 

not be verified independently by USGS, so no loads were 

reported in year 1. During the irrigation season of year 2, loads 

of all constituents were lower at the headworks of the Klamath 

Straits Drain (site KSDH) than at the Klamath Straits Drain 

before it enters the Klamath River, near site KSD97 (table 14). 

In non-irrigation year 2 and all of year 3, loads were zero at 

KSDH, so loads of all constituents were higher at KSD97 

during those periods.

For each of the constituents (TP, TN, BOD5, and 

CBOD5), the sum of the loads at sites ADC97, NC, and KSDH 

(which represents irrigation water coming into the KDD and 

water from the Lower Klamath Wildlife Refuge) can be either 

higher or lower than the load at site KSD97 (near the terminus 

of Klamath Straits Drain before it enters the Klamath River) 

depending on flow conditions. For the non-irrigation period 

in study year 2, TP and TN loads were higher at site KSD97 

than the sum of the loads at sites ADC97, NC, and KSDH 

(table 14), and TP loads were higher during the non-irrigation 

period in year 3. For all other periods, the sum of the TP and 

TN canal loads was higher than the load at site KSD97. This 

suggests that the KDD area can export either more or less 

nutrients into Klamath Straits Drain than it receives depending 

on the hydrologic regime, and that the ability of site KSDH to 

transport constituent loads is poorly characterized in this study 

because the canal was not flowing most of the time.

At site LRDC, water generally flows from the Klamath 

River onto the Klamath Project during irrigation periods, 

and from the project to the Klamath River during the nonirrigation periods. However, in all years of the study, water 

flowed in both directions during irrigation periods, so the 

average instantaneous loads include flows in both positive 

and negative directions. Streamflow during non-irrigation 

periods consistently flowed toward the Klamath River. In 

years 1 and 2, loads of TP and TN flowing toward the Klamath 

River were higher during the non-irrigation period, compared 

to the irrigation period when loads were flowing onto the 

Klamath Project, likely due to the large difference in average 

streamflow (124 and 53.3 ft3/s during non-irrigation periods 

in years 1 and 2, respectively, compared to 15 and 32.4 ft3/s 

during irrigation periods in years 1 and 2, respectively). In 

year three, TP and TN loads were higher during the irrigation 

season compared to loads during the non-irrigation season 

(table 14). 

At site LRDC, BOD5 loads were higher during the 

irrigation season than during the non-irrigation season in 

all 3 years because of the high concentrations of oxygendemanding cyanobacterial biomass from the seasonal 

blooms of AFA in the Klamath River and Upper Klamath 

Lake (table 14). The difference between the two seasons 

was particularly large in years 2 and 3, when the low flows 

of these two drought years resulted in smaller non-irrigation 

period loads than in year 1. CBOD5 loads also were higher 

during the irrigation season than during the non-irrigation 

season in years 2 and 3, indicating that the largest oxygen 

demand was coming from senescence of AFA cells that are 

present in the Klamath River during the summer. However, 

lower CBOD5 loads during the irrigation season than during 

the non-irrigation season in year 1 may indicate that at times, 

high concentrations of ammonia or cellular organic nitrogen 

leaving Upper Klamath Lake contribute a large nitrogenous 

oxygen demand, as well.
Results 41

Table 13. Averaged instantaneous loads at the Tule Lake sites of total phosphorus, total nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous biochemical oxygen demand during irrigation and non-irrigation seasons at sites LREW and PDD, Lost River and Klamath River Basins, northern California, March 2012–March 2015. [Site names and descriptions are shown in table 1; site locations are shown in figure 1. Abbreviations: n, number of instantaneous loads used in the averaging calculation; ND, no data, sd, standard deviation; ft3/s, cubic foot per second; kg/d, kilogram per day]

Site name 

abbreviation

Total phosphorus (TP) Total nitrogen (TN) 5-day biochemical oxygen demand (BOD5) 5-day carbonaceous biochemical oxygen demand (CBOD5) Average streamflow 

(ft3/s) TP (kg/d) n sd TN (kg/d) n sd BOD5 (kg/d) n sd CBOD5 (kg/d) n sd

Irrigation year 1 (201 days) 

LREW ND ND ND ND ND ND ND ND ND ND ND ND NDPPD ND ND ND ND ND ND ND ND ND ND ND ND ND

Non-irrigation year 1 (145 days)

LREW ND ND ND ND ND ND ND ND ND ND ND ND NDPPD ND ND ND ND ND ND ND ND ND ND ND ND ND

Irrigation year 2 (189 days)

LREW 22.2 12 20.5 108 12 103 268 12 266 169 11 161 29.9PPD 18.1 8 51.1 247 8 699 860 8 2,430 944 7 2,500 19.9

Non-irrigation year 2 (168 days)

LREW 10.4 9 11.8 50.1 9 53.2 94.5 7 97.0 89.6 7 88.8 9.34PPD 11.0 11 37.5 139 11 472 622 10 1,970 591 10 1,870 14.2

Irrigation year 3 (195 days)

LREW 23.9 14 25.7 87.3 14 110 241 14 283 193 14 235 25.4PPD 4.74 13 17.1 95.9 13 346 153 13 551 130 13 470 11.1

Non-irrigation year 3 (200 days)

LREW 20.7 14 36.2 106 14 191 201 14 635 160 14 564 17.5PPD 5.84 10 18.5 82.2 10 260 166 10 526 133 10 422 8.12
42 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015 Table 14. Averaged instantaneous loads of total phosphorus, total nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous biochemical oxygen demand during irrigation and non-irrigation seasons at Klamath Drainage District sites (KSDH, ADC97, NC, LRDC, and KSD97) and site LRDC, Lost River and Klamath River Basins, south-central Oregon, March 2012–March 2015. [Positive loads at site LRDC indicate loading to the Lost River, and negative loads indicate loading to the Klamath River. Site names and descriptions are shown in table 1; site locations are shown in figure 1. Abbreviations: n, number of instantaneous loads used in the averaging calculation; NA, not applicable; ND, not data; sd, standard deviation; ft3/s, cubic foot per second; kg/d, kilogram per day] Site name abbreviation Total phosphorus (TP) Total nitrogen (TN) 5-day biochemical oxygen demand (BOD5) 5-day carbonaceous biochemical oxygen demand (CBOD5) Average streamflow (ft3/s) TP (kg/d) n sd TN (kg/d) n sd BOD5 (kg/d) n sd CBOD5 (kg/d) n sd Irrigation year 1 (201 days) KSDH ND ND ND ND ND ND ND ND ND ND ND ND ND ADC97 70.1 13 37.7 709 13 403 2,100 13 1,360 1,510 13 887 177 NC 24.1 14 20.0 221 14 196 720 14 762 535 14 579 54.8 LRDC 3.78 16 84.2 173 16 726 1,400 16 3,920 845 16 2,290 15 KSD97 65.6 14 24.5 466 14 179 1,000 14 584 538 14 278 87 (ADC97+NC+KSDH) - KSD97 28.6 NA NA 464 NA NA 1,820 NA NA 1,507 NA NA NA Non-irrigation year 1 (145 days) KSDH ND ND ND ND ND ND ND ND ND ND ND ND NA ADC97 51.2 10 39.7 559 10 410 907 10 793 696 10 498 131 NC 20.6 10 21.4 197 10 183 271 10 220 267 10 224 49.3 LRDC -93.7 10 138 -536 10 676 -1,130 10 1,940 -1,010 10 1,680 -124 KSD97 42.5 10 53.0 565 10 663 700 10 928 390 10 377 90.2 (ADC97+NC+KSDH) - KSD97 29.3 NA NA 191 NA NA 478 NA NA 573 NA NA NA Irrigation year 2 (189 days) KSDH 16.4 9 44.2 107 9 285 113 9 315 101 8 265 10.9 ADC97 63.0 12 37.3 556 12 324 2,280 11 1,750 1,790 10 1,460 121 NC 20.2 12 19.8 182 12 189 631 12 591 451 11 411 36.7 LRDC 14.8 12 56.6 172 12 582 1,300 12 2,850 1,300 11 3,300 32.4 KSD97 90.7 12 63.6 656 12 455 1,660 12 1,460 1,360 11 1,710 95.5 (ADC97+NC+KSDH) - KSD97 8.90 NA NA 189 NA NA 1,364 NA NA 982 NA NA NA Non-irrigation year 2 (168 days) KSDH 0 11 0 0 11 0 0 11 0 0 11 0 0 ADC97 13.9 12 12.1 191 12 183 389 10 394 347 10 351 54.7 NC 7.01 13 5.43 85.6 13 80.1 193 11 146 191 11 157 26.9 LRDC -18.0 13 14.9 -131 13 125 -271 11 262 -232 11 239 -53.3 KSD97 44.2 12 88.8 389 12 673 340 10 494 320 10 452 52.4 (ADC97+NC+KSDH)– KSD97 -23.3 NA NA -112 NA NA 242 NA NA 218 NA NA NA
Results 43

Table 14. Averaged instantaneous loads of total phosphorus, total nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous biochemical oxygen demand during 

irrigation and non-irrigation seasons at Klamath Drainage District sites (KSDH, ADC97, NC, LRDC, and KSD97) and site LRDC, Lost River and Klamath River Basins, south-central Oregon, March 2012–March 2015.—Continued

Site name 

abbreviation

Total phosphorus (TP) Total nitrogen (TN) 5-day biochemical oxygen demand (BOD5) 5-day carbonaceous biochemical oxygen demand (CBOD5) Average streamflow 

(ft3/s) TP (kg/d) n sd TN (kg/d) n sd BOD5 (kg/d) n sd CBOD5 (kg/d) n sd

Irrigation year 3 (195 days)

KSDH 0 12 0 0 12 0 0 12 0 0 12 0 0

ADC97 22.4 14 36.1 146 14 247 531 14 942 439 14 776 40.1

NC 27.2 14 35.2 200 14 242 736 14 971 674 14 949 38.6

LRDC 49.8 14 64.9 439 14 609 1,510 14 2,660 1,930 14 3,920 78.1

KSD97 26.9 14 36.4 204 14 278 398 14 586 335 14 512 26.9

(ADC97+NC+KSDH)– KSD97 22.7 NA NA 142 NA NA 869 NA NA 778 NA NA NA

Non-irrigation year 3 (200 days)

KSDH 0 13 0 0 13 0 0 13 0 0 13 0 0

ADC97 3.63 14 13.2 27.8 14 101 117 14 430 109 14 402 12.1

NC 12.6 14 11.6 146 14 143 259 13 251 228 13 203 43.1

LRDC -24.3 14 23.8 -223 14 224 -459 14 469 -419 14 470 -53.5

KSD97 16.8 14 38.6 172 14 354 239 14 415 208 14 346 19.7

(ADC97+NC+KSDH)– KSD97 -0.570 NA NA 1.80 NA NA 137 NA NA 129 NA NA NA
44 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

Discussion

Nutrient, 5-Day Biochemical Oxygen Demand, 

and 5-Day Carbonaceous Biochemical Oxygen 

Demand Loading within the Klamath Project

In all years, regardless of irrigation season, upper Lost 

River Basin sites represented the smallest constituent loads 

to the Klamath Project, and site FMT represented the largest 

loads coming into the project. Median concentrations of 

nutrients were similar at the upper Lost River Basin sites 

and site FMT (tables 6–7), but streamflow was much higher 

at site FMT, so the higher loads at FMT primarily are owing 

to higher streamflows. Median concentrations of BOD5 and 

CBOD5 also were similar at the upper Lost River Basin sites 

and site FMT, but peak concentrations of BOD5 and CBOD5

were higher at site FMT during the summer, so the increased 

loads of these constituents are influenced by a combination 

of higher streamflow at site FMT and seasonally high peak 

concentrations of BOD5 and CBOD5. This suggests that Clear 

Lake and Gerber Reservoir did not contribute significant 

amounts of nutrients and BOD5/CBOD5 loads to the project 

during the study period owing to low flows, and that Upper 

Klamath Lake, by contrast, contributes large loads, especially 

during irrigation season when flows are high at site FMT 

(1,440–2,200 ft3/s, table 11), the seasonal algal bloom persists 

in Upper Klamath Lake, and water is being diverted through 

A Canal.

Without directly measuring TP, TN, and BOD5/CBOD5

in A Canal, a true representation of the load partitioning at 

site FMT cannot be achieved, although some approximations 

can be made based on available streamflow data. During 

irrigation season, streamflow reported by Reclamation was 

compared to streamflow calculated at site FMT, resulting in 

about 38 percent of the streamflow at site FMT being diverted 

through A Canal during each study year; for purposes of 

this report, we assume that about 38 percent of the nutrient 

and BOD5/CBOD5 loads also are diverted through A Canal, 

with the remainder flowing down the Link River, into Lake 

Euwana, and to the study site downstream of the Keno Dam 

(site KRK). Along this flowpath, point and nonpoint sources 

of nutrients are sourced from two wastewater treatment 

plants, private industrial timber manufacturing companies, 

stormwater runoff, internal loading from the Klamath 

River, and Klamath Straits Drain and Lost River Diversion 

Channel during non-irrigation periods (Oregon Department of 

Environmental Quality, 2017). The industrial and wastewater 

point sources and stormwater and internal loading contribute 

less TP loads compared to Klamath Straits Drain (Oregon 

Department of Environmental Quality, 2017). If 38 percent of 

TP loads that flow through A Canal are subtracted from the site 

FMT loads, then the resulting reduced TP loads at site FMT 

are slightly smaller during irrigation season in years 1 and 3, 

and larger in year 2, compared to site KRK, suggesting a slight 

increase in TP loads from site FMT to site KRK years 1 and 3 

(table 15). In contrast, if 38 percent of TN, BOD5, and CBOD5

loads are subtracted from the site FMT loads, the remaining 

loads are still higher at site FMT compared to site KRK during 

irrigation season (with the exception of non-irrigation year 3), 

indicating that the Klamath Project is not a large source of TN 

or oxygen-demanding material and that much of the oxygen 

demand in the river at site FMT has been expressed by the 

time the same water passes through site KRK.

Table 15. Average of modeled mean daily loads (using LOADEST) 

of total phosphorus, total nitrogen, 5-day biochemical oxygen 

demand, and 5-day carbonaceous biochemical oxygen demand 

during irrigation seasons to account for A Canal diversions at 

sites KRK and FMT, including a 38-percent reduction in loads at 

site FMT, south-central Oregon, March 2012–March 2015.

[Loads at site FMT during irrigation season include a 3-percent reduction 

to account for A Canal diversions. Site names and descriptions are shown in 

table 1; site locations are shown in figure 1. Abbreviation: kg/d, kilogram per 

day]

Site name 

abbreviation

Total 

phosphorus 

(kg/d)

Total 

nitrogen 

(kg/d)

Biochemical oxygen demand 

(kg/d)

5-day 5-day 

carbonaceous

Irrigation year 1 

FMT 450 4,706 18,414 16,306

KRK 527 4,450 9,750 7,410

Non-irrigation year 1

FMT 111 1,870 3,700 3,150

KRK 172 2,060 3,670 3,040

Irrigation year 2

FMT 344 3,714 15,004 13,516

KRK 302 2,760 6,980 5,410

Non-irrigation year 2

FMT 120 1,950 3,990 3,390

KRK 188 2,220 4,270 3,470

Irrigation year 3

FMT 328 3,565 14,384 12,896

KRK 344 3,070 7,430 5,740

Non-irrigation year 3

FMT 110 1,780 3,690 3,150

KRK 176 2,100 4,110 3,350
Discussion 45

In most years during non-irrigation periods, TP and TN 

loads computed with LOADEST at the end-members sites 

consistently showed a small increase in TP and TN loads along 

the flowpath from sites FMT to KRK (table 11). Because there 

are no diversions of water from site FMT through A Canal 

during non-irrigation periods, the only nutrient inputs that 

could be causing this increase in nutrient loads are the point 

and nonpoint sources described in the previous paragraph 

and internal loading from sediments, with the addition of 

inputs from the Klamath Straits Drain and the Lost River 

Diversion Channel. The Lost River Diversion Channel 

represents nonpoint sources of nutrients from the Klamath 

Project, natural runoff from the upper Lost River Basin, and 

stormwater runoff from the city of Klamath Falls. 

Data on loads entering and leaving Tule Lake during 

study years 2 and 3 show similar loads of TP, TN, BOD5, and 

CBOD5 along the flowpath from the lower Lost River to Pump 

Plant D (site PPD), regardless of irrigation or non-irrigation 

seasons. The water-quality dynamics in this area of the project 

are not adequately characterized because of the low volume of 

samples collected at site PPD. However, for the few samples 

that were collected, sample concentrations can be discussed. 

Increases in BOD5/CBOD5 concentrations from Tule Lake 

to site PPD in year 2 of the study are likely attributed to the 

high DOC concentrations also observed at site PPD (table 9). 

This form of organic carbon is different than the particulate 

algal carbon observed at site FMT, which represents biomass 

from Upper Klamath Lake that has an oxygen demand 

when the algae decompose. The organic carbon composition 

observed at site PPD suggests a fresh, slightly decomposed 

carbon that could originate from sources such as animal 

manure or algal exudates based on low humification index 

values, which show the relative contribution of terrestrial or 

microbial sources of organic matter (Goldman and Sullivan, 

2017). Higher humification index values typically indicate 

an increasing rate of carbon decomposition. Additionally, 

the high DOC concentrations present at sites downstream of 

the inundated wetlands of Tule Lake and the Lower Klamath 

Wildlife Refuge also could be owing to molecular diffusion of 

DOC resulting from the inundation of peat soils (Aguilar and 

Thibodeaux, 2005).

Nutrient Budget for Klamath River from 

Link River Dam to Keno Dam

Considering nutrient, BOD5, and CBOD5 loads at the 

two boundary sites (sites FMT and KRK), all canal diversions 

from the Klamath River (NC, ADY, and LRDC during 

irrigation season) and drains into the Klamath River (KSD97 

year-round and LRDC during non-irrigation season) between 

the boundary sites, a nutrient balance can be calculated to 

examine the change in loads from sites FMT to KRK. Loads 

either entering or leaving the Klamath River main stem 

between the boundary sites, and mean loads at the boundary 

sites for irrigation and non-irrigation periods for all 3 years 

of the study, are shown in figures 20–22 and table 16. The 

loads shown at site FMT in figures 20–22 include a 38-percent 

reduction to account for A Canal loads entering the Klamath 

Project during irrigation season, and the “NET” value is 

calculated as the site FMT reduced load subtracting the 

canal diversions (shown as negative loads in figures 20–22

to represent a load reduction from the Klamath River) and 

adding the drains (shown as positive loads to represent load 

additions to the river). The “NET” value, therefore, represents 

the mean load in the Klamath River downstream of where the 

Klamath Straits Drain enters the river. Site LRDC is shown as 

a negative load relative to the Klamath River during irrigation 

years, when water is flowing from the river to the Klamath 

Project, and as a positive load during non-irrigation seasons, 

when water is flowing from the project to the Klamath River.

A noticeable consistent pattern in the load balance 

shows that, during irrigation season in all 3 years of the study, 

the NET load for all constituents downstream of Klamath 

Straits Drain is lower than the load at site FMT before all the 

diversions, drains, and point sources along the Klamath River 

(figs. 20–22). The average percent differences during the three 

irrigation seasons comparing the site FMT load to the NET 

load for TP and TN were -10 and -12 percent, respectively, 

and the corresponding average percent differences for BOD5

and CBOD5 were both -17 percent (table 16). During nonirrigation periods, the NET loads were higher compared to 

site FMT, and the differences were larger for TP and TN than 

BOD5 and CBOD5. Between sites FMT and KRK during 

non-irrigation periods, TP loads increased by an average of 

38 percent, TN loads increased by an average of 14 percent, 

BOD5 loads increased by an average of 9 percent, and CBOD5

loads increased by an average of 8 percent, respectively 

(table 16). These load differences suggest that, during 

irrigation season in the 3 years of the study period, more loads 

are being diverted from the Klamath River than are being 

added to the Klamath River from the combination of Klamath 

Straits Drain, regulated point sources along the Klamath 

River, and internal loading from the bottom sediments in the 

river. By contrast, during non-irrigation seasons, more loads 

are being added to the Klamath River than are being diverted 

through Ady and North Canals, and this difference primarily 

is owing to additional loads to the River from the Lost River 

Diversion Channel. 
46 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-1203_fig 20

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

−100

 0

 100

 200

 300

 400

 500

 600

−100

 0

 100

 200

 300

 400

 500

 600

−1,000

0

1,000

2,000

3,000

4,000

5,000

−4,000

0

4,000

8,000

12,000

16,000

20,000

−4,000

0

4,000

8,000

12,000

16,000

20,000

−1,000

1,000

2,000

3,000

4,000

5,000

−4,000

4,000

8,000

12,000

16,000

20,000

−4,000

4,000

8,000

12,000

16,000

20,000

0

0

0

Mean TP load,

in kilograms per day

Mean TP load,

in kilograms per day

Mean TN load,

in kilograms per day

Mean TN load,

in kilograms per day

Mean BOD5 load,

in kilograms per day

Mean BOD5 load,

in kilograms per day

Mean CBOD5 load,

in kilograms per day

Mean CBOD5 load,

in kilograms per day

Irrigation year 1 Non-irrigation year 1

Figure 20. Total phosphorus, total nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous 

biochemical oxygen demand loads along the Klamath River flowpath from sites FMT to KRK, south-central 

Oregon, March 2012–13 (study year 1). Site names and descriptions are shown in table 1; site locations are 

shown in figure 1. “NET” refers to reduced site FMT load calculated by subtracting the canal diversions 

(negative loads in figure) and adding the drains (positive loads in figure excluding site KRK).
Discussion 47

tac18-1203_fig 21

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

−100

 0

 100

 200

 300

 400

 500

 600

−100

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

−1000

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

 0

 100

 200

 300

 400

 500

 600

−1,000

0

1,000

2,000

3,000

4,000

5,000

0

1,000

2,000

3,000

4,000

5,000

−4,000

0

4,000

8,000

12,000

16,000

20,000

−4,000

0

4,000

8,000

12,000

16,000

20,000

−4,000 −4,000

0

4,000

8,000

12,000

16,000

20,000

0

4,000

8,000

12,000

16,000

20,000

Mean TP load,

in kilograms per day

Mean TP load,

in kilograms per day

Mean TN load,

in kilograms per day

Mean TN load,

in kilograms per day

Mean BOD5 load,

in kilograms per day

Mean BOD5 load,

in kilograms per day

Mean CBOD5 load,

in kilograms per day

Mean CBOD5 load,

in kilograms per day

Irrigation year 2 Non-irrigation year 2

Figure 21. Total phosphorus, total nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous 

biochemical oxygen demand loads along the Klamath River flowpath from sites FMT to KRK, south-central 

Oregon, March 2013–14 (study year 2). Site names and descriptions are shown in table 1; site locations are 

shown in figure 1. “NET” refers to reduced site FMT load calculated by subtracting the canal diversions 

(negative loads in figure) and adding the drains (positive loads in figure excluding site KRK).
48 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-1203_fig 22

−100

 0

 100

 200

 300

 400

 500

 600

Mean TP load,

in kilograms per day

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

−100

 0

 100

 200

 300

 400

 500

 600

Mean TP load,

in kilograms per day

−1,000

0

1,000

2,000

3,000

4,000

5,000

Mean TN load,

in kilograms per day

−1,000

0

1,000

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

FMT LRDC NC ADC97 KSD97 NET KRK FMT LRDC NC ADC97 KSD97 NET KRK

1,000

2,000

3,000

4,000

5,000

Mean TN load,

in kilograms per day

−4,000

0

4,000

8,000

12,000

16,000

20,000

Mean BOD5 load,

in kilograms per day

Mean BOD5 load,

in kilograms per day

0

4,000

8,000

12,000

16,000

20,000

−4,000

0

4,000

8,000

12,000

16,000

20,000

−4,000

0

4,000

8,000

12,000

16,000

20,000

Mean CBOD5 load,

in kilograms per day

Mean CBOD5 load,

in kilograms per day

Irrigation year 3 Non-irrigation year 3

Figure 22. Total phosphorus, total nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous 

biochemical oxygen demand loads along the Klamath River flowpath from sites FMT to KRK, south-central 

Oregon, March 2014–15 (study year 3). Site names and descriptions are shown in table 1; site locations are 

shown in figure 1. “NET” refers to reduced site FMT load calculated by subtracting the canal diversions 

(negative loads in figure) and adding the drains (positive loads in figure excluding site KRK).
Discussion 49

Table 16. Nutrient load and streamflow balance using average of modeled mean daily loads (using LOADEST) total phosphorus, 

total nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous biochemical oxygen demand at sites KRK and FMT, 

and average of daily loads at sites LRDC, NC, ADC97, and KSD97, south-central Oregon, March 2012–March 2015.

[Loads and streamflow at site FMT during irrigation season include a 38-percent reduction to account for A Canal diversions as noted. Positive loads at 

site LRDC indicate loading to the Lost River, and negative loads indicate loading to the Klamath River. Positive numbers in the “Balance” row indicate 

more nutrients or streamflow at site KRK compared to the net nutrient load and streamflow of all project diversions from, and inputs to, the Klamath 

River. Site names and descriptions are shown in table 1; site locations are shown in figure 1. Abbreviations: ft3/s, cubic feet per second ; kg/d, kilogram 

per day, %, percent]

Site name abbreviation

Total 

phosphorus

(kg/d)

Total 

nitrogen

(kg/d)

Biochemical oxygen demand 

(kg/d) Average daily

streamflow

(ft3 5-day /s) 5-day 

carbonaceous

Irrigation year 1 

FMT with A Canal reduction 450 4,706 18,414 16,306 1,364

LRDC 3.78 173 1,400 845 15

NC 24.1 221 720 535 54.8

ADC97 70.1 709 2,100 1,510 177

KSD97 65.6 466 1,000 538 87

NET [FMT-sum(LRDC, NC, ADC97)+KSD97] 418 4,069 15,194 13,954 1,204

Percent difference NET-FMT -7% -14% -17% -14% -12%

KRK 527 4,450 9,750 7,410 1,291

Balance 109 381 -5,444 -6,544 87

Percent difference NET-KRK 26% 9% -36% -47% 7%

Non-irrigation year 1

FMT with A Canal reduction 111 1,870 3,700 3,150 406

LRDC -93.7 -536 -1,130 -1,010 -124

NC 20.6 197 271 267 49.3

ADC97 51.2 559 907 696 131

KSD97 42.5 565 700 390 90.2

NET [FMT-sum(LRDC, NC, ADC97)+KSD97] 175 2,215 4,352 3,587 440

Percent difference NET-FMT 58% 18% 18% 14% 8%

KRK 172 2,060 3,670 3,040 678

Balance -3 -155 -682 -547 238

Percent difference NET-KRK -2% -7% -16% -15% 54%

Irrigation year 2

FMT with A Canal reduction 344 3,714 15,004 13,516 918

LRDC 14.8 172 1,300 1,300 32.4

NC 20.2 182 631 451 36.7

ADC97 63 556 2,280 1,790 121

KSD97 90.7 656 1,660 1,360 95.5

NET [FMT-sum(LRDC, NC, ADC97)+KSD97] 337 3,460 12,453 11,335 823

Percent difference NET-FMT -2% -7% -17% -16% -10%

KRK 302 2,760 6,980 5,410 689

Balance -35 -700 -5,473 -5,925 -134

Percent difference NET-KRK -10% -20% -44% -52% -16%

Non-irrigation year 2

FMT with A Canal reduction 120 1,950 3,990 3,390 443

LRDC -18 -131 -271 -232 -53.3

NC 7.01 85.6 193 191 26.9

ADC97 13.9 191 389 347 54.7

KSD97 44.2 389 340 320 52.4

NET [FMT-sum(LRDC, NC, ADC97)+KSD97] 161 2,193 4,019 3,404 467

Percent difference NET-FMT 34% 12% 1% 0% 5%

KRK 188 2,220 4,270 3,470 739

Balance 27 27 251 66 272

Percent difference NET-KRK 17% 1% 6% 2% 58%
50 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

Table 16. Nutrient load and streamflow balance using average of modeled mean daily loads (using LOADEST) total phosphorus, 

total nitrogen, 5-day biochemical oxygen demand, and 5-day carbonaceous biochemical oxygen demand at sites KRK and FMT, 

and average of daily loads at sites LRDC, NC, ADC97, and KSD97, south-central Oregon, March 2012–March 2015. —Continued

Site name abbreviation

Total 

phosphorus

(kg/d)

Total 

nitrogen

(kg/d)

Biochemical oxygen demand 

(kg/d) Average daily

streamflow

(ft3 5-day /s) 5-day 

carbonaceous

Irrigation year 3

FMT with A Canal reduction 328 3,565 14,384 12,896 893

LRDC 49.8 439 1,510 1,930 78.1

NC 27.2 200 736 674 38.6

ADC97 22.4 146 531 439 40.1

KSD97 26.9 204 398 335 26.9

NET [FMT-sum(LRDC, NC, ADC97)+KSD97] 255 2,984 12,005 10,188 763

Percent difference NET-FMT -22% -16% -17% -21% -15%

KRK 344 3,070 7,430 5,740 772

Balance 89 86 -4,575 -4,448 9

Percent difference NET-KRK 35% 3% -38% -44% 1%

Non-irrigation year 3

FMT with A Canal reduction 110 1,780 3,690 3,150 405

LRDC -24.3 -223 -459 -419 -53.5

NC 12.6 146 259 228 43.1

ADC97 3.63 27.8 117 109 12.1

KSD97 16.8 172 239 208 19.7

NET [FMT-sum(LRDC, NC, ADC97)+KSD97] 135 2,001 4,012 3,440 423

Percent difference NET-FMT 23% 12% 9% 9% 4%

KRK 176 2,100 4,110 3,350 695

Balance 41 99 98 -90 272

Percent difference NET-KRK 30% 5% 2% -3% 64%

Average percent difference NET-FMT, 

irrigation season

-10% -12% -17% -17% -12%

Average percent difference NET-FMT, 

non-irrigation season

38% 14% 9% 8% 6%

In some years, the differences between loads at the 

Link River Dam (represented as the loads at site FMT with a 

38-percent reduction to account for A Canal diversions) and 

the NET load downstream of Klamath Straits Drain were 

small. This is particularly noticeable in BOD5 and CBOD5

loads during non-irrigation season in years 2 and 3 of the 

study, where percent differences were 0 and 1 percent in 

non-irrigation year 2 and 9 percent for non-irrigation year 

3. Percent differences in BOD5 and CBOD5 loads in the 

year 1 non-irrigation season were higher (18 and 14 percent, 

respectively) than in years 2 and 3, likely owing to the higher 

streamflows at site LRDC when it was flowing toward the 

Klamath River in year 1 compared to years 2 and 3.

Closing the loop on the nutrient balance for the Klamath 

River requires a comparison of the loads at site KRK, 

the lower boundary of the study, to the NET load after all 

measured loads to the canals and from drains are accounted 

for. The differences between site KRK and the NET value 

are shown as “Balance” in table 16, and can be assessed 

graphically by comparing the “NET” and “KRK” load bars 

in figures 20–22. Positive numbers in the “Balance” row in 

table 16 indicate more loads measured at site KRK than the 

calculated NET load, and negative numbers indicate less 

loads measured at site KRK than the calculated NET load. 

Positive balance numbers suggest that there is additional 

loading in the system, such as internal cycling from river 

bottom sediments and point sources, which is not accounted 

for in the large canals supplying nutrient loads to the Klamath 

River. A positive or negative balance also can be an indication 

of the error in the load estimates, particularly in the canals. 

Numerous individual diversions from the Klamath River 

along this flowpath were not characterized by this study, and 

also could be reducing loads in the river. The occurrence and 

magnitude of differences between site KRK and the NET 

loads were variable and showed few consistent patterns for 

load constituents and the irrigation/non-irrigation season. One 
Discussion 51

consistent pattern was that BOD5 and CBOD5 loads were 

consistently lower at KRK than the calculated NET value 

during irrigation season in all 3 study years. This discrepancy 

likely is the result of the oxygen demand being expressed 

within the water column from the decay of the AFA biomass 

along this flowpath during summer in the irrigation season. 

It also is possible that the loads diverted from the Klamath 

River were underestimated because of individual diversions 

that were not assessed for this study, or that the loads coming 

into the Klamath River from site KSD97 were overestimated 

during irrigation season. However, these individual load 

values are small compared to the overall loads measured at 

site FMT with the 38 percent A Canal reduction, so these 

differences also could be owing to uncertainty in the load 

estimates at site FMT from the LOADEST model. 

The LOADEST models used to calculate BOD5 and 

CBOD5 loads at site FMT greatly underestimated the peak 

loads that occurred during June–August in the 3 study years 

(fig. 18), so the loads for site FMT reported in table 16 for the 

irrigation periods are assumed to be biased low. If we assume 

that the loads are higher than reported from the LOADEST 

model, the conclusions of the nutrient balance do not change, 

but the magnitude of the differences would change, making 

the “NET” value reported in table 16 and figures 20–22 larger 

than shown. For the BOD5 and CBOD5 loads, this means that 

there would be a larger difference in the NET value compared 

to KRK during irrigation season, which could mean that more 

oxygen demand is expressed in the reach between Link River 

and Keno Dams than is shown in these figures. For the TP 

and TN loads, the NET value would be closer to the value 

reported at site KRK, which means that the canal diversions 

and nutrient input from Klamath Straits Drain explain most of 

the change in nutrient loads along this stream reach.

Organic Carbon and Nitrogen

Changes in the concentration of DOC and TPC along 

the Lost River-Tule Lake-Klamath Straits Drain flow path 

have been measured in this study for the few samples 

collected when the flowpath was hydrologically connected, 

and especially notable are changes between the inflow and 

outflow of Tule Lake, where concentrations of DOC, TPC, and 

TPN all increased from sites LREW to PPD. These relations 

are not well characterized because of the small volume of 

samples collected at site PPD. For purposes of this report, 

TPC is assumed to be primarily composed of organic carbon at 

KSD97 based on previous work that has shown non-detectable 

levels of particulate inorganic carbon for the Klamath Straits 

Drain and other sites on the Klamath River between the Link 

River and Keno Dams (Sullivan and others, 2010).

The highest concentrations of TPN occurred at sites that 

divert water directly from the Klamath River (sites FMT, 

ADC97, LRDC(+)), which likely is owing to particulate algae 

at those sites from seasonal blooms of AFA. However, only 

site ADC97 showed a positive correlation of chlorophyll-a, 

the biomass surrogate for AFA, with TPN (R2=0.76, p<0.05). 

High concentrations of chlorophyll-a present at site FMT 

(the south end of Upper Klamath Lake) often were not 

concurrently sampled for TPN because of the infrequent 

nature (every 6 weeks) of constituent sampling for organic 

carbon and nitrogen during the study.

Nutrient Loads and Total Maximum Daily Loads

The Oregon Department of Environmental Quality 

sets nonpoint source load allocations of pollutants that can 

contribute to a stream without exceeding State water-quality 

standards. TP, TN, and BOD5 loads have been identified as 

causing non-compliance of water quality standards for pH, 

dissolved oxygen, ammonia toxicity and chlorophyll-a in the 

Klamath River (Oregon Department of Environmental Quality, 

2017). The two primary sources of water to the Klamath 

River from the Klamath Project are the Klamath Straits 

Drain and Lost River Diversion Channel. Klamath Straits 

Drain exceeded TMDL load allocations for TP and TN in all 

3 study years (March 2012–March 2015; table 2), but only 

exceeded TMDL load allocations for BOD5 in years 1 and 2, 

as indicated by averages of instantaneous daily loads during 

the study period (fig. 23). At site LRDC, TP loads exceeded 

TMDL load allocations in all three study years, TN loads 

exceeded TMDL load allocations in year 1 only, and BOD5

loads were less than the TMDL load allocations for all three 

study years (fig. 24).

Suggestions for Future Studies

The persistent drought conditions during all years of 

the study resulted in many sample events when sites did not 

have measurable streamflow. As a result, the number of data 

points used to estimate loads at some sites was unacceptably 

small—for example, sites KSDH and PPD. Therefore, this 

study was unable to assess contributions of nutrients to the 

Klamath River under typical conditions, so some of the study 

conclusions may not be reproducible in out years beyond 

this study that have normal flow regimes. Long-term data 

collection efforts would allow for better representation of a 

range of flow regimes, and hydrologic and meteorological 

conditions. Additionally, biweekly, scheduled sampling events 

often can miss important runoff events, especially in the 

upper Lost River Basin, where some sites have substantial 

unregulated drainage and thus respond to precipitation events. 

A combination of scheduled and storm-event sampling would 

better characterize the range of constituent concentrations, 

loads, and streamflow at the sample sites. Additionally, close 

coordination with Reclamation to plan sampling events 

when water at sites KSDH and PPD is flowing would allow 

for better characterization of water quality from these sites. 
52 Nutrient Loads in the Lost River and Klamath River Basins, South-Central Oregon and Northern California, 2012–2015

tac18-0777_fig 23

Klamath Straits Drain at Highway 97

 0

10

20

30

40

50

60

70

80

90

TMDL

0

100

200

300

400

500

600

TMDL

600

400

200

0

800

1,000

1,400

1,200

TMDL

Average total phosphorus (TP) load, in kilograms per day

Average total nitrogen (TN) load, in kilograms per day

Average biochemical oxygen demand (BOD5) load, in kilograms per day

Year 1 Year 2 Year 3 Year 1 Year 2 Year 3 Year 1 Year 2 Year 3

Figure 23. Average daily loads of total phosphorus, total nitrogen, and 5-day biochemical oxygen demand and Total Maximum 

Daily Load (TMDL) load allocations at site KSD97, south-central Oregon. Site name and description are shown in table 1; site 

location is shown in figure 1.

 0

10

20

30

40

50

60

70

80

90

TMDL

1,200

TMDL

Lost River Diversion Channel

Average total phosphorus (TP) load, in kilograms per day

Average total nitrogen (TN) load, in kilograms per day

Average biochemical oxygen demand (BOD5) load, in kilograms per day

0

100

200

300

400

500

600

600

400

200

0

800

1,000

1,400

TMDL

Year 1 Year 2 Year 3 Year 1 Year 2 Year 3 Year 1 Year 2 Year 3

Figure 24. Average daily loads of total phosphorus, total nitrogen, and 5-day biochemical oxygen demand, and Total Maximum 

Daily Load (TMDL) load allocations at site LRDC, south-central Oregon. Site name and description are shown in table 1; site 

location is shown in figure 1.
References Cited 53

An improved characterization in the form of streamgages 

that record continuous streamflow at some of the ungaged 

project sites also will allow for better load estimates. This 

additional information is critical in understanding waterquality dynamics in the Klamath Straits Drain, and Tule Lake 

in particular.

The direct measurement of constituent loads diverted 

through A Canal also is an important missing component to 

this study, as the diversion of water through the canal greatly 

affects the computation of load allocations downstream of the 

Link River Dam. A sampling program that conducts separate 

assessments of A Canal and the Link River downstream of the 

A Canal diversion would reduce the uncertainty of constituent 

load assessments at this important boundary of the Klamath 

Project.

LOADEST model results for BOD5 and CBOD5 at sites 

FMT and KRK showed a low bias of loads during irrigation 

season, although these differences were more extreme for the 

seasonal wave models at FMT. The low bias suggests that 

the LOADEST model is not adequately capturing the cause 

of the variability in BOD5 and CBOD5, the source of which 

primarily is the large biomass from AFA blooms in Upper 

Klamath Lake that are transported downstream in the latter 

part of the summer. Alternative models, such as the USGS 

EGRET (Exploration and Graphics for RivEr Trends) model, 

may provide for better description of this process as that 

model describes long-term averages, the patterns of variability, 

and temporal trends (Hirsch and De Cicco, 2015). The 

EGRET model involves three components—(1) evaluation of 

streamflow statistics; (2) graphical display of water-quality 

sample data as they vary in relation to time, discharge, or 

season; and (3) application of the Weighted Regressions on 

Time, Discharge, and Season (WRTDS) smoothing method, 

which can identify changes that are specific to particular 

seasons of the year (Hirsch and De Cicco, 2015). In addition 

to these models, continuous water-quality parameters collected 

on the Klamath River at the Link River Dam and upstream 

of the Keno Dam also can be evaluated as surrogates, either 

independently or in conjunction with the alternative models, to 

provide for a more accurate assessment of nutrient, BOD5, and 

CBOD5 loads.

Acknowledgments

We acknowledge the assistance of Eric Janney and 

many personnel at the U.S. Geological Survey Klamath Falls 

Field Station for facilitating data collection efforts, including 

Robert Blake, Thomas Craig, Blake Eldridge, Charles Goebel, 

Douglas Labonte, Alex Lee, Celeste Melosh, and Bradley 

Smith for their efforts collecting and processing water-quality 

samples and streamflow measurements. We also thank the 

reviewers who provided constructive comments that improved 

this document. 

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Appendix 1 55

Appendix 1. Loadest Model Summaries for Rejected Models

Appendix 1 is a PDF file and is available for download at https://doi.org/10.3133/sir20185075.

Publishing support provided by the U.S. Geological Survey

Science 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

2130 SW 5th Avenue

Portland, Oregon 97201

https://www.usgs.gov/centers/or-water
Schenk and others—Nutrient Loads, Lost and Klamath River Basins, South-Central Oregon and California, 2012–15—Scientific Investigations Report 2018-5075

ISSN 2328-0328 (online)

https://doi.org/10.3133/sir20185075