U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2020–5096

Prepared in cooperation with the U.S. Environmental Protection Agency

Before remediation: May 2014. After remediation: June 2020.

Trends in Concentrations, Loads, and Sources of Trace 

Metals and Nutrients in the Spokane River Watershed, 

Northern Idaho, Water Years 1990–2018
Cover.

Left photograph (before): Waste piles at Success Mine adjacent to East Fork of Ninemile Creek 

before remediation, May 2014. 

Right photograph (after): Graded and re-vegetated hill at Success Mine after remediation, June 2020.

Photographs by the Successor Coeur d’Alene Custodial and Work Trust.
Trends in Concentrations, Loads, and 

Sources of Trace Metals and Nutrients in 

the Spokane River Watershed, Northern 

Idaho, Water Years 1990–2018

By Lauren M. Zinsser

Prepared in cooperation with the U.S. Environmental Protection Agency

Scientific Investigations Report 2020–5096

U.S. Department of the Interior

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

DAVID BERNHARDT, Secretary

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2020

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Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials 

as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested citation:

Zinsser, L.M., 2020, Trends in concentration, loads, and sources of trace metals and nutrients in the Spokane 

River Watershed, northern Idaho, water years 1990-2018: U.S. Geological Survey Scientific Investigations Report 

2020–5096, 58 p., https://doi.org/10.3133/sir20205096.

ISSN 2328-0328 (online)
iii

Contents

Abstract...........................................................................................................................................................1

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

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

Study Site Description .........................................................................................................................3

Constituent Transport ...........................................................................................................................5

Approaches for Load Calculation and Trend Detection .................................................................5

Methods...........................................................................................................................................................6

Data Collection ......................................................................................................................................6

Streamflow Data ..........................................................................................................................6

Water-Quality Data for Water Years 1990–2003 ....................................................................10

Water-Quality Data for Water Years 2004–18 ........................................................................11

Analyses...............................................................................................................................................11

Ambient Water-Quality Criteria ...............................................................................................11

Streamflow Trends .....................................................................................................................12

Water Quality: Concentrations, Loads, and Trends ..............................................................12

Results ...........................................................................................................................................................17

Streamflow Stationarity .....................................................................................................................16

Quality Control Samples ....................................................................................................................18

Comparisons to Ambient Water-Quality Criteria ...........................................................................19

Model Performance............................................................................................................................23

Trends in Concentrations and Loads ...............................................................................................27

Zinc...............................................................................................................................................30

Cadmium ......................................................................................................................................31

Lead..............................................................................................................................................33

Nutrients ......................................................................................................................................38

Spatial Patterns in Load Sources .....................................................................................................41

South Fork Coeur d’Alene River ..............................................................................................41

Coeur d’Alene River ...................................................................................................................41

Coeur d’Alene Lake ...................................................................................................................42

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

Metals...................................................................................................................................................45

Nutrients...............................................................................................................................................47

Topics for Additional Study ...............................................................................................................50

Summary........................................................................................................................................................50

Acknowledgments.......................................................................................................................................51

References Cited..........................................................................................................................................52

Appendix 1 Summary Graphs Showing Weighted Regressions on Time, Discharge and 

Season (WRTDS) and Weighted Regressions on Time, Discharge and Season 

with Kalman Filtering (WRTDS_K) Modeled Annual Concentrations and Loads ................57

Appendix 2 Model Diagnostics ..............................................................................................................58
iv

Figures

1. Maps showing study area and sampling sites, Spokane River watershed, 

northern Idaho...............................................................................................................................4

2. Quantile-Kendall plots showing trends in streamflow for water years 1990–2018 

for select sites in the Spokane River watershed, northern Idaho ......................................17

3. Boxplots showing dissolved zinc ambient water-quality criteria ratios for water 

years 1990–2018 for sites in the Spokane River watershed, northern Idaho ...................20

4. Boxplots showing dissolved cadmium ambient water-quality criteria ratios for 

water years 1990 –2018 for sites in the Spokane River watershed, northern Idaho .......24

5. Boxplots showing dissolved lead ambient water-quality criteria ratios for water 

years 1990–2018 for sites in the Spokane River watershed, northern Idaho ...................25

6. Box plots showing flux bias statistics associated with Weighted Regressions 

on Time, Discharge and Season models for water years 1990-2018, grouped by 

parameter and site, Spokane River watershed, northern Idaho .......................................26

7. Boxplots showing annual mean concentrations and loads for cadmium, lead 

and zinc from Weighted Regressions on Time, Discharge and Season with 

Kalman filtering models for water years 2014–18 for sites in the Spokane River 

watershed, northern Idaho .......................................................................................................28

8. Graphs showing dissolved zinc annual mean concentrations and annual total 

loads from Weighted Regressions on Time, Discharge and Season with Kalman 

filtering and flow-normalized annual mean concentrations and annual total 

loads from Weighted Regressions on Time, Discharge and Season for select 

sites in the Spokane River watershed, northern Idaho, water years 1990–2018 .............31

9. Schematic showing statistical likelihood and magnitude of change in 

flow-normalized dissolved zinc concentrations and annual total loads over 

the period of record and water years 2009–18 for sites in the Spokane River 

watershed, northern Idaho .......................................................................................................32

10. Graphs showing change in load per year and 90 percent confidence intervals 

for select constituents and sites in the Spokane River watershed, northern Idaho .......33

11. Graphs showing dissolved cadmium annual mean concentrations and annual 

total loads from Weighted Regressions on Time, Discharge and Season with 

Kalman filtering and flow-normalized annual mean concentrations and annual 

total loads from Weighted Regressions on Time, Discharge and Season for 

select sites in the Spokane River watershed, northern Idaho ............................................34

12. Schematic showing statistical likelihood and magnitude of change in 

flow-normalized dissolved cadmium concentrations and loads over the period 

of record and water years 2009–18 for sites in the Spokane River watershed, 

northern Idaho .............................................................................................................................35

13. Graphs showing total lead annual mean concentrations and annual total loads 

from Weighted Regressions on Time, Discharge and Season with Kalman 

filtering and flow-normalized annual mean concentrations and annual total 

loads from Weighted Regressions on Time, Discharge and Season for select 

sites in the Spokane River watershed, northern Idaho ........................................................36

14. Graphs showing statistical likelihood and magnitude of change in 

flow-normalized total lead concentrations and loads over the period of record 

and water years 2009–18 for sites in the Spokane River watershed, northern Idaho ....37
v

15. Graphs showing total phosphorus annual mean concentrations and annual 

total loads from Weighted Regressions on Time, Discharge and Season with 

Kalman filtering and flow-normalized annual mean concentrations and annual 

total loads from Weighted Regressions on Time, Discharge and Season for 

select sites in the Spokane River watershed, northern Idaho, water years 

1990-2018......................................................................................................................................39

16. Schematics showing statistical likelihood and magnitude of change in 

flow-normalized total phosphorus concentrations and loads over the period 

of record and water years 2009–18 for sites in the Spokane River watershed, 

northern Idaho .............................................................................................................................40

17. Graphs showing incremental annual total loads for sites in the South Fork 

Coeur d’Alene River, northern Idaho, water years 1999–2018 ...........................................42

18. Graphs showing incremental annual total loads for the South Fork Coeur 

d’Alene River, the North Fork Coeur d’Alene River, and the main-stem Coeur 

d’Alene River, northern Idaho, water years 1994–2018 ........................................................43

19. Graphs showing annual total loads into and out of Coeur d’Alene Lake, 

northern Idaho, water years 2005–18 .....................................................................................44

Tables

1. Streamgaging and water-quality monitoring sites and data used for analyses, 

Spokane River watershed, northern Idaho ..............................................................................7

2. Example ambient water-quality criteria for different sample hardness, South 

Fork Coeur d’Alene River-specific and Idaho state-wide criteria ......................................12

3. Summary of site, parameters, water years, and samples used for Weighted 

Regressions on Time, Discharge and Season (WRTDS) and WRTDS with 

Kalman filtering (WRTDS_K) models, and flux bias statistics for WRTDS models ..........14

4. Statistical likelihood descriptors ..............................................................................................16

5. Summary of blank sample results, water years 1997–2018 .................................................18

6. Summary of replicate sample results, water years 1997–2018 ...........................................19

7. Median ambient water-quality criteria ratios for dissolved cadmium, lead 

and zinc, water years 1990–2018, for sites in the Spokane River watershed, 

northern Idaho .............................................................................................................................21

8. Five year mean of annual mean concentrations for total and dissolved 

constituents derived from Weighted Regression on Time, Discharge and 

Season with Kalman filtering models for sites in the Spokane River watershed, 

northern Idaho, water years 2014–18 ......................................................................................29
vi

Conversion Factors

U.S. customary units to International System of Units

Multiply By To obtain

Length

mile (mi) 1.609 kilometer (km)

Area

square mile (mi2) 2.590 square kilometer (km2)

Flow rate

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

Volume

liter (L) 0.2642 gallon (gal)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

kilogram (kg) 2.205 pound avoirdupois (lb)

metric ton (t) 1.102 ton, short [2,000 lb]

metric ton (t) 0.9842 ton, long [2,240 lb]

Datums

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

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

Elevation, as used in this report, refers to distance above the vertical datum.

Supplemental Information

Concentrations of chemical constituents in water are given in micrograms per liter (μg/L).
vii

Abbreviations

ADVM acoustic Doppler velocity meter

AWQC ambient water-quality criteria

CDR Coeur d’Alene River

EGRET Exploration and Graphics for RivEr Trends

EPA U.S. Environmental Protection Agency

NFCDR North Fork Coeur d’Alene River

SFCDR South Fork Coeur d’Alene River

USGS U.S. Geological Survey

WRTDS Weighted Regressions on Time, Discharge and Season

WRTDS_K Weighted Regressions on Time, Discharge and Season with Kalman filtering

WY water year
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Trends in Concentrations, Loads, and Sources of Trace 

Metals and Nutrients in the Spokane River Watershed, 

Northern Idaho, Water Years 1990–2018

By Lauren M. Zinsser

Abstract

A long history of mining and widespread metals contamination in the Coeur d’Alene River watershed and downstream 

into the Spokane River has led to the area’s designation as a 

Superfund site and to extensive, ongoing (as of 2020) remedial actions. Long-term water-quality and streamflow data, 

collected by the U.S. Geological Survey for up to 29 years at 

20 sampling sites in the Coeur d’Alene, Spokane and St. Joe 

River watersheds, were analyzed to evaluate the impact of 

remedial actions on metals in surface water. Analyses focused 

on total and dissolved cadmium, zinc and lead. Trends in total 

phosphorus, total nitrogen and dissolved orthophosphate were 

also evaluated; although these nutrients are not constituents of 

concern for the Superfund site, they are important to the health 

of Coeur d’Alene Lake.

Dissolved cadmium, zinc and lead concentrations 

were compared to ambient water-quality criteria at 20 

sample sites. For the 12 sites with the most extensive data 

records, Weighted Regressions on Time, Discharge and 

Season (WRTDS) models were developed to estimate flownormalized annual mean concentrations and flow-normalized 

annual total loads; these results were used to evaluate trends 

because flow-normalization dampens the impact of interannual 

streamflow variability on concentrations and loads. WRTDS 

models with Kalman filtering (WRTDS_K) were developed to 

estimate annual mean concentrations and annual total loads; 

these results were used to evaluate spatial patterns in constituent sources. Models were developed for total and dissolved 

cadmium, lead, and zinc; total phosphorus and nitrogen; and 

dissolved orthophosphate, although not all constituents were 

modeled for all sites due to limited sample sizes. Bootstrapped 

confidence intervals were constructed to determine the 

statistical likelihood of trends and the slope of trends in 

flow-normalized concentrations and loads during the period 

of record (13–29 years, depending on the site), water years 

1999–2009, and water years 2009–18. 

A feature of trend analysis with WRTDS is the ability 

to translate the outcomes of the likelihood statistical tests 

into plain language. As used throughout this report, a trend 

was considered “likely up” when the likelihood statistic was 

between 0.85 and 1.0; that is, when the probability that the 

trend is up was greater than or equal to 0.85. Conversely, a 

trend with a likelihood statistic of 0 to 0.15 was considered 

“likely down” because a low probability that a trend is up is 

equivalent to a high probability that the trend is actually down. 

A trend was “somewhat likely up” when the likelihood statistic was between 0.70 and 0.85, and “somewhat likely down” 

for values between 0.15 and 0.30. Finally, a trend was considered “about as likely as not” – essentially a statistical toss-up 

– when the likelihood statistic was between 0.30 and 0.70.

Total and dissolved cadmium and zinc concentrations and 

loads have decreased with high statistical likelihood at virtually all mining-affected sites over both the period of record 

and water years 2009-18. During the period of record, total 

and dissolved zinc and cadmium concentrations and loads 

decreased about 25-75 percent with “likely down” trends. The 

decreases in total and dissolved zinc and cadmium concentrations and loads persisted with high statistical likelihood 

(“likely down” trends) during water years 2009-18 although 

the absolute magnitude of the decreases was lower (about 

10-30 percent). The magnitude of ambient water-quality 

criteria exceedances for dissolved cadmium, zinc and lead 

also decreased at most mining-affected sites over the period of 

record, though concentrations remain above chronic criteria at 

most sites. 

Although trend analyses inherently cannot ascribe causality, the trends in metals are consistent with processes of metal 

transport and the occurrence of remedial actions across the 

Superfund site. Early remedial actions focused on removing 

source materials from streams and floodplains in the South 

Fork Coeur d’Alene River and tributaries; the removal of these 

primary and stream-proximal materials aligns with the period 

of steepest declines in metals concentrations and loads. Slower 

decreases in metals concentrations and loads in water years 

2009-18 suggest that remedial actions continue to positively 

impact water quality but that pervasive secondary sources of 

metals (for example, in groundwater and fluvial sediments) 

may be responding more slowly. Thus, trend analyses are 

strong evidence that extensive remedial actions across the 

Superfund site have improved water quality at most sites 

through reductions in cadmium and zinc.
2 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

Total and dissolved lead concentrations and loads have 

also decreased at most mining-affected sites over the period 

of record and during water years 2009–18. At most miningaffected sites, total and dissolved lead concentrations and 

loads had “likely down” trends of about 20–85 percent over 

the period of record and had “likely down” or “somewhat 

likely down” trends of about 10–50 percent during water 

years 2009–18. However, “somewhat likely up” trends for 

total lead occurred in the Coeur d’Alene River near Harrison 

over the period of record. These results suggest that source 

removals for particulate lead in the upper parts of the Coeur 

d’Alene River watershed have resulted in decreasing total lead 

loads for most sites, but substantial remaining particulate lead 

sources lower in the watershed (where major removal actions 

have not yet begun) continue to affect water quality in the 

main-stem Coeur d’Alene River.

Incremental load analyses illustrate patterns in metal 

sources across the study area, and point to areas that may 

warrant investigation for potential future remedial actions. 

Substantial loading of total lead in the South Fork Coeur 

d’Alene River above Elizabeth Park may be related to tailings 

in Osburn Flats. The incremental annual total loads for the 

Coeur d’Alene River near Harrison (which was considered a 

proxy for total load delivered to Coeur d’Alene Lake) indicate 

that the South Fork Coeur d’Alene River remained the source 

of the majority of dissolved zinc and cadmium loads to Coeur 

d’Alene Lake, whereas the main-stem Coeur d’Alene River 

remained the source of the majority of the total and dissolved 

lead loads. Widely dispersed particulate contaminants in the 

river beds, banks, and floodplains of the main-stem Coeur 

d’Alene River system are a continuing source of particulate 

metals during high streamflows and, in conjunction with 

geochemical processes, are also a continuing source of dissolved metals. Future remedial actions in the main-stem Coeur 

d’Alene River are being planned to address these sources.

Trends in total phosphorus were temporally and spatially 

variable in the study area over the analysis period. Total phosphorus concentrations and loads had “likely up” or “somewhat 

likely up” trends in the South Fork Coeur d’Alene River near 

Pinehurst and Coeur d’Alene River near Harrison over the 

period of record but had “likely down” or “somewhat likely 

down” load trends at these sites during water years 2009–18. 

Differences in the magnitude of the change and river characteristics at these sites, and a lack of trends in other parts of the 

study area, suggest that local processes and mechanisms may 

be most important for driving trends. Analysis of the incremental annual total loads at these sites shows that the biggest 

total phosphorus loads occur during high streamflows years, 

which indicates that the main phosphorus sources are active 

during runoff conditions. In the steeper, more developed South 

Fork Coeur d’Alene River floodplain, trends could be related 

to surface runoff that has decreased over time due to remedial 

actions to stabilize hillslopes and increase riparian vegetation. 

In the productive, low-gradient main-stem Coeur d’Alene 

River, trends could be related to channel changes following 

near-record flooding in the 1990s that made total phosphorus 

more accessible for transport in the 2000s. However, interpretation of the total phosphorus trends is fundamentally limited 

by sparse datasets and a lack of mechanistic understanding of 

nutrient transport in the study area.

In summary, robust trend analyses of long-term waterquality monitoring data suggest that remedial actions have 

decreased metal concentrations and loads in the Coeur 

d’Alene and Spokane Rivers during both longer (13–29 years) 

and more recent (2009–18) periods. Sites with increasing or 

unclear trends in concentrations and loads, particularly for 

total lead, and spatial patterns in contaminant loading, may 

point to areas for focusing future remedial efforts.

Introduction

The Coeur d’Alene River watershed has a long and 

complicated history of mining, metals transport, and remedial 

activities. Once a globally important source of silver, lead, and 

zinc, mining in the Coeur d’Alene district began in the late 

1800s and continues today (2020), having produced millions 

of metric tons of lead and zinc and over a billion ounces of silver (Springer, 1997; Gillerman, 2019). Long (1998) estimated 

that production of the ore generated 109 million metric tons 

of mill tailings waste, of which about 56 million metric tons 

were “disposed of or otherwise lost into the Coeur d’Alene 

River or its tributaries” prior to cessation of direct dumping in 

1968. These metal-laced tailings, containing zinc, cadmium, 

lead, arsenic, and copper, are widely dispersed throughout 

the Coeur d’Alene River fluvial system, including tributaries, 

the main-stem Coeur d’Alene River floodplain, the bottom of 

Coeur d’Alene Lake, and downstream into the Spokane River. 

Additional mine-related wastes also remain pervasive on land 

surfaces throughout the Coeur d’Alene River watershed as a 

direct result of hundreds of mining operations, the redistribution of metals-contaminated sediment via natural and humancaused processes, and the historical reuse of waste materials 

as road beds, railroad ballast, and fill (Long, 1998; U.S. 

Environmental Protection Agency, 2002, 2012b).

Listed by the U.S. Environmental Protection Agency 

(EPA) on the National Priorities List in 1983 (U.S. 

Environmental Protection Agency, 1992), the affected area 

is formally named the Bunker Hill Mining and Metallurgical 

Complex Superfund Site (hereinafter, “the Bunker Hill 

Superfund Site”). Collectively, the Bunker Hill Superfund 

Site encompasses all areas of the Coeur d’Alene and Spokane 

River watersheds affected by mining-related contamination, an 

area which stretches across the northern Idaho panhandle and 

into eastern Washington (fig. 1). Although multiple contaminants of concern have been identified by the various Records 

of Decision (U.S. Environmental Protection Agency, 1992, 

2002, 2012b), this report focuses on total and dissolved zinc, 

cadmium, and lead. These metals occur at high concentrations in surface waters throughout the Bunker Hill Superfund 

Site and have long been recognized (U.S. Environmental 
Introduction 3

Protection Agency, 1992) and prioritized for remedial actions 

(U.S. Environmental Protection Agency, 2002). This report 

also presents analyses for total phosphorus, total nitrogen, 

and dissolved orthophosphate. None of these nutrients were 

identified as a contaminant of concern in the various Records 

of Decisions, but they are of particular interest because of 

their importance to maintaining the health of Coeur d’Alene 

Lake (Idaho Department of Environmental Quality and 

Coeur d'Alene Tribe, 2009). Approximately 75 million metric 

tons of metals-contaminated sediment lie on the bottom 

of Coeur d’Alene Lake (Horowitz and others, 1995). The 

2002 Record of Decision did not select a remedy for Coeur 

d’Alene Lake (U.S. Environmental Protection Agency, 2002), 

instead deferring to the development of the Coeur d’Alene 

Lake Management Plan, which aims to limit nutrients entering the lake in order to maintain oxygenated bottom water 

and therefore prevent mobilization of metals from benthic 

sediments (Idaho Department of Environmental Quality and 

Coeur d'Alene Tribe, 2009). Recent analyses indicate that total 

phosphorus concentrations are increasing in Coeur d’Alene 

Lake (Idaho Department of Environmental Quality and Coeur 

d'Alene Tribe, 2019), heightening concern about nutrient 

trends in the Coeur d’Alene Lake watershed.

Remedial actions at the Bunker Hill Superfund Site 

began in 1989, guided by a series of Record of Decision documents and associated technical studies (U.S. Environmental 

Protection Agency, 2012a). Given the scope and complexity 

of metals contamination in the Bunker Hill Superfund Site, 

the EPA is following an adaptive management approach and 

refraining from selecting final remedies in some areas (U.S. 

Environmental Protection Agency, 2002; National Research 

Council of the National Academies, 2005; U.S. Environmental 

Protection Agency, 2012b). As part of the adaptive management approach, the EPA works with various entities to conduct 

extensive monitoring of various media throughout the Coeur 

d’Alene River watershed. This report addresses one component of this effort by describing long-term trends based on 

surface water monitoring.

Purpose and Scope

The U.S. Geological Survey (USGS) has conducted 

streamgaging and water-quality monitoring in the Coeur 

d’Alene, Spokane, and St. Joe River watersheds (hereinafter, “the study area”) in cooperation with the EPA and other 

entities since 1990. This report, which incorporates all these 

data, focuses on the statistical analysis of and description of 

trends from water year1 (WY) 1990 through 2018, focusing 

on select metals (total and dissolved cadmium, lead, and zinc) 

and nutrients (total phosphorus, total nitrogen, and dissolved 

orthophosphate). These analyses build on an extensive body 

1A water year starts October 1 of the previous calendar year and ends 

September 30.

of previous works that described metal transport mechanisms, 

concentration and loading attributes, and trends in the study 

area from WY 1990 through WY 2013. The analyses in this 

report sought to address how remedial actions in the Bunker 

Hill Superfund Site are affecting key metals by asking if concentrations and loads are going down and if spatial patterns in 

load sources are changing. 

Study Site Description

The Spokane River watershed comprises the Coeur 

d’Alene River (CDR) and St. Joe River watersheds. The 

main-stem CDR is formed at the confluence of its two 

major branches (fig. 1), the North Fork Coeur d’Alene River 

(NFCDR) and the South Fork Coeur d’Alene River (SFCDR). 

The CDR watershed stretches from the Idaho-Montana border 

in the east to Coeur d’Alene Lake near the Idaho-Washington 

border in the west, draining about 1,465 square miles with 

a mean watershed elevation of 3,730 feet. Most of the CDR 

watershed is forest with steep, narrow valleys. The Spokane 

River flows west from the outlet of Coeur d’Alene Lake. The 

other major tributary to Coeur d’Alene Lake is the St. Joe 

River, which is unaffected by mining, has one major branch 

(St. Maries River), and drains about 1,730 square miles with 

a mean watershed elevation of 4,070 feet. Most of the St. Joe 

River watershed is steep forest, similar to the CDR watershed 

(U.S. Geological Survey, 2016c).

The Coeur d’Alene mining district is primarily within 

the SFCDR watershed but also includes parts of the NFCDR 

watershed (Long, 1998). Mineralization in the district occurs 

in veins hosted in metasedimentary rocks of the Proterozoic 

Belt Supergroup, with galena, sphalerite, and tetrahedrite 

being among the most important ore-bearing minerals. Ore 

deposits occur in a strongly folded and faulted shear zone 

and are offset by two major strike-slip faults–the Osburn and 

Placer Creek faults (Fryklund and Weis, 1964).

Remedial actions in the non-populated portions of the 

Bunker Hill Superfund Site began in 1992 and have been 

varied and extensive throughout the SFCDR, main-stem CDR, 

and in SFCDR tributaries including Canyon, Ninemile, and 

Pine Creeks. While most actions have been completed by the 

EPA, other entities such as the Bureau of Land Management 

and mine owners have also conducted some cleanup activities, particularly in Canyon Creek and Pine Creek. Actions 

from 1992 to present (2020) have included hillside excavation, terracing, and revegetation; the capping and covering 

of the Central Impoundment Area; removal, stabilization 

or capping of tailings from streambanks and land surfaces; 

upgrades to the Central Treatment Plant; water treatment pilot 

projects; and the demolition of mine and mill structures (U.S. 

Environmental Protection Agency, 2012a)
4 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

95

90

90

90

90

97

5

3

Coeur d'Alene 

mining district

Central 

impoundment 

area Central 

treatment plant

St. Joe River

Pine Creek

Big Creek

e

Pine Creek

Big Creek

Pine Creek

St. Maries

 River 

North Fork

Coeur d'Alene River 

Canyon Creek 

Spokane River 

Bunker Creek

Milo Creek

Government Gulch

Coeur d'Alene 

Lake

Lake 

Hayden

Ninemile

Creek

Ninemile 

Creek

Canyon Creek

East Fork

Ninemile Creek

South Fork Coeur d'Alene River

Coeur d'Alene River

South Fork Coeur d'Alene River

South Fork Coeur d'Alene River

North Fork Coeur d'Alene River

Coeur d'Alene River

East Fork Pine Creek

Pinehurst

Smelterville

Kellogg

Kellogg

Osburn

Mullan

Pinehurst

Cataldo

Wallace

Wardner

SHOSHO

NE

BE

NEWA

H

Coeur d'Alene Mountains

St. Joe Mountains

BITTERROOT RANGE

Cataldo

Post Falls

Coeur d'Alene

Kellogg

Harrison

Osburn

Plummer

Pinehurst

St. Maries

Wardner

IDAHO

WASHIG

TON

MONTANA

SHOSHO

NE

KOOTENAI BE

NEWA

H

Post 

Falls 

Dam

Wallace Mullan

MONTANA

CDR near

Harrison CDR at

Rose Lake

St. Joe River at Ramsdell

CDR near

Cataldo

Pine Creek

NFCDR at

Enaville

SFCDR near

Pinehurst

SFCDR above

Pine Creek

SFCDR at

Smelterville

SFCDR at

Kellogg

Seeps north 

of tailings

Government

Gulch

Milo

Creek

Bunker

Creek

SFCDR at

Elizabeth Park

SFCDR at Wallace

Ninemile

Creek Canyon

Creek

SFCDR near

Mullan

Spokane River

below lake outlet

St. Joe River

St. Maries River at Calder

at Santa

Spokane River

near Post Falls

IDAHO

WASHINGTON

WASHINGTON

OREGON

MONTANA

Study

 area

EXPLANATION

Monitoring site and site name

City limits

Base from U.S. Geological Survey digital data

USA Contiguous Albers Equal Area Conic USGS version

North American Datum of 1983 0 10 KILOMETERS

0 10 MILES

Base from U.S. Geological Survey digital data

USA Contiguous Albers Equal Area Conic USGS version

North American Datum of 1983 0 5 KILOMETERS

0 5 MILES

0 1 KILOMETER

Base map from National Agricultural Imagery Program 0 1 MILE

Hydrology from National Hydrology Dataset Plus

117°00' 30' 116°00' 115°30'

47°

30'

47°

45'

47°

15'

116°15' 116°00' 115°45'

47°

30'

47°

35'

Figure 1. Study area and sampling sites, Spokane River watershed, northern Idaho. The Bunker Hill Superfund Site 

comprises locations within the watershed where mining-related contamination is located. CDR, Coeur d’Alene River; NFCDR, 

North Fork Coeur d’Alene River; SFCDR, South Fork Coeur d’Alene River.
Introduction 5

Constituent Transport

Previous works have established the major patterns of 

streamflow and metal and nutrient concentrations, loads, 

and transport in the study area. Loads represent the total 

mass (measured in kilograms or metric tons) of a constituent 

conveyed through a point over an interval of time (per day 

or per year). Both concentrations and loads are important for 

understanding trends in the study area. Constituent concentrations directly affect aquatic organisms and can be compared to 

water-quality criteria and some remedial action benchmarks to 

assess long-term changes. Loads are helpful for understanding the sources and delivery timing of constituents and for 

understanding the total mass of constituents moving downstream and entering Coeur d’Alene Lake. The CDR and St. 

Joe River contribute roughly similar amounts of streamflow 

and total phosphorus loads to Coeur d’Alene Lake (Maupin 

and Weakland, 2009; Clark and Mebane, 2014), but the CDR 

is the source of virtually all metals (Clark, 2003; Clark and 

Mebane, 2014). Within the CDR, the NFCDR contributes 

roughly 70 percent of total streamflow (versus 30 percent from 

the SFCDR), while the SFCDR contributes over 90 percent 

of the total cadmium, zinc, and lead load, as measured in the 

CDR near the confluence of the NFCDR and SFCDR (Clark, 

2003; Donato, 2006; Clark and Mebane, 2014). However, 

while the SFCDR is the source of most of the cadmium and 

zinc load in the CDR, most of the lead load comes from the 

main-stem CDR between the confluence near Cataldo and 

the outlet near Harrison (Clark, 2003; Clark and Mebane, 

2014). Although the biggest loads of zinc, cadmium, and lead 

are transported during high streamflow events, the highest 

concentrations of zinc and cadmium (which occur primarily in 

the dissolved form) occur during low streamflow conditions in 

both the SFCDR and main-stem CDR (Clark, 2003; Clark and 

Mebane, 2014). Lead occurs primarily in the particulate form, 

and high streamflow events (particularly rain-on-snow winter 

flood events) have historically transported both the highest 

concentrations and loads of lead (Beckwith, 1996; Clark and 

Mebane, 2014). Similar to total lead, the highest concentrations and loads of total phosphorus occur during flood and runoff events (Idaho Department of Environmental Quality and 

Coeur d'Alene Tribe, 2019). Particulate zinc and cadmium also 

become a more important part of the total zinc and cadmium 

loads in the SFCDR and CDR during high streamflow events 

(Clark and Mebane, 2014).

Approaches for Load Calculation and Trend 

Detection

Multiple previous works have used the LOAD ESTimator (LOADEST) software package (U.S. Geological Survey, 

2016b) to estimate metal and nutrient loads and concentrations in the study area over 5–10 year intervals (Clark, 2003; 

Donato, 2006; Wood and Beckwith, 2008; Clark and Mebane, 

2014). The LOADEST model uses maximum likelihood 

regression to develop regression relationships between concentration, discharge, time, and season (Runkel and others, 

2004). The sign and significance of the coefficients associated 

with time can be interpreted as representing change in concentration in a stream over time (Donato, 2006), but the LOADEST model fundamentally relies on the assumption that the 

shape of the underlying relationships (for example, between 

concentration and discharge) remains constant over time. 

This assumption becomes problematic for long-term analyses 

where the relationship between concentration and the predictor 

variables can change. For example, this issue could be particularly important where remedial measures might have had a 

profound effect on concentrations during high flow events but 

little effect at low flow (or vice-versa). The LOADEST model 

is not able to capture such differences and the failure to do so 

can confound interpretations of the changes taking place.

The recent development of the Weighted Regressions on 

Time, Discharge and Season (WRTDS) modeling approach 

and subsequent enhancements have sought to address some of 

the limitations of conventional load models such as LOADEST (Hirsch and others, 2010). Fundamentally a weighted 

regression model, WRTDS develops a time-varying linear 

relationship between log-transformed concentrations and 

explanatory variables (time, discharge, and season) by creating 

a unique regression between the variables for each day in the 

period of study. Thus, WRTDS is a highly flexible model that 

allows the relationships between concentration, discharge, 

and season to change gradually over time (Hirsch and others, 

2010). The resulting model can then be used to explore trends 

in flow-normalized concentrations and loads over various 

time periods, such as years, seasons, or months (Sprague and 

others, 2011). Flow-normalization is an important component 

of the method because it removes the influence of year-to-year 

variation in streamflow. This greatly enhances the ability of 

the method to identify trends (by increasing the signal to noise 

ratio) and protects the analysis from being highly influenced 

by the random occurrence of a particularly wet or dry year 

near the end or the beginning of the period of study (Sprague 

and others, 2011). The WRTDS model is implemented 

by using the Exploration and Graphics for RivEr Trends 

(EGRET) package (Hirsch and De Cicco, 2015) for R (R Core 

Team, 2019).

The initial implementation of WRTDS relied on the 

assumption that, although the relationship between discharge 

and concentration may change, the underlying distribution of discharges remained stationary (Hirsch and others, 

2010). While this is often a reasonable assumption over short 

time periods, it can break down over longer periods of trend 

analysis when land use changes or climate impacts influence 

patterns of discharge. A recently developed extension of the 

EGRET package created a series of tools to evaluate trends 

in discharge over the period of interest (Hirsch, 2018) and 

developed a method to partition the impact of changes in 

discharge versus the importance of other explanatory variables 

in contributing to an observed trend in concentration or load 

(Choquette and others, 2019).
6 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

Other subsequent works related to WRTDS have created 

tools to describe biases in WRTDS load and concentration 

estimates (Hirsch, 2014); developed a method to estimate 

uncertainty associated with trends from WRTDS (Hirsch 

and others, 2015); and implemented Kalman filtering within 

WRTDS (Zhang and Hirsch, 2019). The Kalman filtering 

enhancement uses actual sample concentrations in place of 

estimates for days in the study period with water-quality 

samples. This generally has the net effect of improving the 

accuracy of load and concentration estimates for specific days, 

seasons, or years (Lee and others, 2019; Zhang and Hirsch, 

2019). Accordingly, a new extension of WRTDS, WRTDS_K, 

was created to implement the Kalman filtering (Hirsch, 2019).

Recent publications have compared the performance of 

conventional load estimation methods (including LOADEST) 

to the newer WRTDS and WRDTS_K methods (Hirsch, 2014; 

Lee and others, 2016; Lee and others, 2017; Lee and others, 

2019). Each load estimation method is capable of producing 

accurate load and concentration estimates (Lee and others, 

2016; Lee and others, 2019), but WRTDS_K is generally most 

likely to produce the most accurate estimates (Lee and others, 

2019). Previous studies in the study area have determined 

that, over the time period considered in this report (approximately 15–30 years), multiple constituents show substantial 

trends, and constituents have complicated relationships to 

streamflow (Clark and Mebane, 2014). Given these challenges 

and the results of recent method comparisons, WRTDS and 

WRTDS_K models were selected for this study. Specifically, 

WRTDS was used to estimate flow-normalized annual 

mean concentrations and annual total loads and to explore 

and describe trends because the flow-normalized estimates 

increase the signal-to-noise ratio by removing variation due 

to differences in streamflow. In contrast, WRTDS_K was used 

to make the best estimates of annual mean concentrations and 

annual total loads because these models more fully utilize the 

available sample information.

Methods

Data Collection

The USGS has been collecting water-quality and streamflow data in the study area under various programs with different cooperators for several decades. Relatively consistent 

water-quality sample collection and continuous streamgaging 

at several sites in the study area began in WY 1990. Analysis 

of long-term datasets are powerful for analyzing trends, but 

compiling and checking such datasets can be challenging 

because of inevitable changes in sample collection procedures 

and sampling strategies, lab analysis techniques, precision 

and accuracy, data management, and more. Impacts of such 

changes that are pertinent to this study are explored in the 

“Water-Quality Data” and “Quality Control Samples” sections. Table 1 summarizes the USGS sites used in various 

analyses in this report, including which type of data were used 

from each site, noting where site data were combined to yield 

longer records and describing the abbreviated site names used 

hereinafter. This report uses “site” to refer to water-quality 

sampling locations and continuous streamgaging locations. 

Note that “streamflow,” “discharge,” and “flow” have equivalent meaning in this report, but “discharge” is only used when 

referring to eponymous statistical or gaging techniques, and 

“flow” is only used when referring to flow-normalized results.

Streamflow Data

The USGS has operated continuous streamgages in the 

study area over a variety of timescales, with some streamgaging sites dating back to 1911 (NFCDR at Enaville) and others 

installed as recently as 2014 (Spokane River below Blackwell 

near Coeur d’Alene). Gage records also differ in continuity 

because operations were not necessarily continuous for each 

gage and there are record gaps of various lengths at some 

sites. Streamgaging sites on the SFCDR, NFCDR, tributaries, 

and the CDR near Cataldo use conventional stage-discharge 

relationships to estimate continuous streamflow (Sauer and 

Turnipseed, 2010; Turnipseed and Sauer, 2010). Streamgaging 

sites for the CDR near Harrison, the St. Joe River at Ramsdell, 

and the Spokane River below lake outlet are affected by 

backwater conditions for part of the year due to the operation 

of a hydroelectric dam on the Spokane River downstream of 

Coeur d’Alene Lake. These gaging sites use index velocity 

methods to estimate continuous streamflow (Levesque and 

Oberg, 2012).

In 2002, the USGS formally adopted the use of acoustic 

Doppler velocity meters (ADVMs) to produce continuous 

streamflow records (Morlock and others, 2002). ADVMs measure stream velocity in two dimensions and use those measurements along with an index velocity relationship to estimate 

streamflow (Levesque and Oberg, 2012). This method can be 

particularly useful in channels that are prone to backwatering 

effects where traditional stage-discharge relationships often 

break down (Morlock and others, 2002; Levesque and Oberg, 

2012). Following the widespread implementation of this 

technique, the USGS installed three ADVM continuous gage 

systems in the study area in the early 2000s: one in the CDR 

near Harrison, one in the St. Joe River at Ramsdell, and one in 

the Spokane River below lake outlet. Each of these locations 

is prone to backwater effects; thus, the installation of these 

ADVM gages marks the first time that continuous stream gage 

records were available for these locations.
Methods 

7

Table 1. Streamgaging and water-quality monitoring sites and data used for analyses, Spokane River watershed, northern Idaho.[Site number: Throughout this report, “site” is used refer to water-quality sampling locations and continuous streamgaging locations. To improve data quality, Spokane River site 12417620 was moved about a mile downstream to 12417650 and St. Joe River site 12415140 but was moved about 1.5 miles upstream to 12415135. Abbreviations: NFCDR, North Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River; CDR, Coeur d'Alene River]

Site number Site name (formal)

Site name (short, 

as used in this 

report)

Latitude 

(decimal 

degrees)

Longitude 

(decimal 

degrees)

Drainage 

area 

(square 

miles)

Types and uses of site data

Long-term 

streamflow 

analysis

WRTDS and 

WRTDS_K 

models

12413000 North Fork Coeur 

d'Alene River at Enaville, Idaho

NFCDR at 

Enaville

47.5722 -116.2528 895 Continuous streamflow and 

water-quality samples

Yes Yes

12413040 South Fork Coeur 

d'Alene River above Deadman Gulch near Mullan, Idaho

SFCDR near 

Mullan

47.4733 -115.7665 17.3 Instantaneous streamflow and 

water-quality samples

No No

12413125 Canyon Creek above 

mouth at Wallace, Idaho

Canyon Creek 47.4725 -115.9147 22.0 Continuous streamflow (partial 

record) and water-quality samples

No Yes

12413130 Ninemile Creek above 

mouth at Wallace, Idaho

Ninemile Creek 47.4749 -115.9227 11.6 Continuous streamflow (partial 

record) and water-quality samples

No Yes

12413131 South Fork Coeur 

d'Alene River above Placer Creek at Wallace, Idaho

SFCDR at 

Wallace

47.4752 -115.9284 84.5 Continuous streamflow and 

water-quality samples

No No

12413210 South Fork Coeur 

d'Alene River at Elizabeth Park near Kellogg, Idaho

SFCDR at 

Elizabeth Park

47.5314 -116.0925 182 Continuous streamflow and 

water-quality samples; index station for 12413125, 12413130, 12413250, and 12413300 synthetic hydrographs

No Yes

12413250 South Fork Coeur 

d'Alene River (at Bunker Avenue) at Kellogg, Idaho

SFCDR at 

Kellogg

47.5453 -116.1342 194 Instantaneous streamflow and 

water-quality samples

No Yes

12413290 Government Gulch 

Creek near mouth at Smelterville, Idaho

Government 

Gulch

47.5438 -116.1668 3.0 Instantaneous streamflow and 

water-quality samples

No No

12413300 South Fork Coeur 

d'Alene River at Smelterville, Idaho

SFCDR at 

Smelterville

47.5483 -116.1753 202 Instantaneous streamflow and 

water-quality samples

No Yes
8 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin Table 1. Streamgaging and water-quality monitoring sites and data used for analyses, Spokane River watershed, northern Idaho.—Continued

[Site number: Throughout this report, “site” is used refer to water-quality sampling locations and continuous streamgaging locations. To improve data quality, Spokane River site 12417620 was moved about a mile downstream to 12417650 and St. Joe River site 12415140 but was moved about 1.5 miles upstream to 12415135. Abbreviations: NFCDR, North Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River; CDR, Coeur d'Alene River]

Site number Site name (formal)

Site name (short, 

as used in this 

report)

Latitude 

(decimal 

degrees)

Longitude 

(decimal 

degrees)

Drainage 

area 

(square 

miles)

Types and uses of site data

Long-term 

streamflow 

analysis

WRTDS and 

WRTDS_K 

models

12413355 South Fork Coeur 

d'Alene River above Pine Creek near Pinehurst, Idaho

SFCDR above 

Pine Creek

47.5483 -116.2197 207 Continuous streamflow and 

water-quality samples

No No

12413370 East Fork Pine Creek 

above Nabob Creek near Pinehurst, Idaho

East Fork Pine 

Creek

47.4767 -116.2217 28.2 Continuous streamflow; index 

station for 12413445 synthetic hydrograph

No No

12413445 Pine Creek below Amy 

Gulch near Pinehurst, Idaho

Pine Creek 47.5081 -116.2418 73.2 Continuous streamflow (partial 

record) and water-quality samples

No Yes

12413470 South Fork Coeur 

d'Alene River near Pinehurst, Idaho

SFCDR near 

Pinehurst

47.5519 -116.2364 287 Continuous streamflow and 

water-quality samples

Yes Yes

12413500 Coeur d'Alene River near 

Cataldo, Idaho

CDR near 

Cataldo

47.5547 -116.3231 1,208 Continuous streamflow and 

water-quality samples

Yes Yes

12413810 Coeur d'Alene River at 

Rose Lake, Idaho

CDR at Rose 

Lake

47.5375 -116.4722 1,318 Instantaneous streamflow and 

water-quality samples

No No

12413860 Coeur d'Alene River near 

Harrison, Idaho

CDR near 

Harrison

47.4786 -116.7331 1,453 Continuous streamflow and 

water-quality samples; modeled streamflow from Donato (2006) used prior to March 2004

No Yes

12414500 St. Joe River at Calder, 

Idaho

St. Joe River at 

Calder

47.2744 -116.1889 1,025 Continuous streamflow Yes No

12414900 St. Maries River near 

Santa, Idaho

St. Maries River 

near Santa

47.1761 -116.4933 273 Continuous streamflow Yes No

12415135 St. Joe River at Ramsdell 

near St. Maries, Idaho

St. Joe River at 

Ramsdell

47.3522 -116.6756 1,721 Continuous streamflow (partial 

record) and water-quality samples (partial record)

No Yes
Methods 

9

Table 1. Streamgaging and water-quality monitoring sites and data used for analyses, Spokane River watershed, northern Idaho.—Continued[Site number: Throughout this report, “site” is used refer to water-quality sampling locations and continuous streamgaging locations. To improve data quality, Spokane River site 12417620 was moved about a mile downstream to 12417650 and St. Joe River site 12415140 but was moved about 1.5 miles upstream to 12415135. Abbreviations: NFCDR, North Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River; CDR, Coeur d'Alene River]

Site number Site name (formal)

Site name (short, 

as used in this 

report)

Latitude 

(decimal 

degrees)

Longitude 

(decimal 

degrees)

Drainage 

area 

(square 

miles)

Types and uses of site data

Long-term 

streamflow 

analysis

WRTDS and 

WRTDS_K 

models

12415140 St. Joe River near 

Chatcolet, Idaho

NA 47.3613 -116.6916 1,727 Continuous streamflow (partial 

record) and water-quality samples; streamflow and waterquality records combined with 12415135

No No

12417610 Spokane River below 

lake outlet at Coeur d'Alene, Idaho

Spokane River 

below lake outlet

47.6819 -116.7975 3,700 Continuous streamflow (partial 

record) and water-quality samples (partial record)

No Yes

12417620 Spokane River at 

Highway 95 crossing at Coeur d'Alene, Idaho

NA 47.6860 -116.7996 3,701 Water-quality samples (partial 

record); water-quality records combined with 12417610

No No

12417650 Spokane River below 

Blackwell near Coeur d'Alene, Idaho

NA 47.6947 -116.8153 3,702 Continuous streamflow (partial 

record); streamflow records combined with 12417610

No No

12419000 Spokane River near Post 

Falls, Idaho

Spokane River 

near Post Falls

47.7031 -116.9778 3,830 Continuous streamflow; streamflow records combined with 

12417610

Yes No

473210116070601 Milo Creek outfall at 

South Fork Coeur d'Alene River at Kellogg, Idaho

Milo Creek 47.5366 -116.1198 4.2 Instantaneous streamflow and 

water-quality samples

No No

473252116095301 Bunker Creek at mouth 

of culvert at Kellogg, Idaho

Bunker Creek 47.5472 -116.1656 2.8 Instantaneous streamflow and 

water-quality samples

No No

473254116091200 Seeps north of 

Deadwood Gulch tailings at Kellogg, Idaho

Seeps north of 

tailings

47.5483 -116.1534 NA Instantaneous streamflow and 

water-quality samples

No No
10 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

These locations have nonetheless been challenging.

As table 1 shows, the original Spokane River ADVM 

streamgaging site was at 12417620, but it was moved about 

a mile downstream to 12417650 to improve the data quality. Similarly, the original St. Joe River gaging site was at 

12415140, but it was moved about 1.5 miles upstream to 

12415135 to improve data quality. In both cases, the streamflow records from both sites on each river have been combined 

for the analyses in this report to generate a longer streamflow record.

At sites without continuous stream gages, measurements 

or estimates of streamflow have generally been made at the 

time of water-quality sample collection. Measurement of 

streamflow followed standard USGS procedures (Rantz, 1982; 

Oberg and others, 2005; Mueller and others, 2013). During 

some flooding and runoff events, it was more important to 

collect as many water-quality samples as close in time as possible to capture specific hydrologic and transport conditions 

than to take synchronous streamflow measurements. For these 

events, streamflow at sites without gaging sites was sometimes 

estimated after the fact based on the relationship between the 

ungaged site and a proximal, continuously gaged site. These 

streamflow records are marked with an “E” for “estimated” 

in the National Water Information System (U.S. Geological 

Survey, 2020).

For many water-quality analyses, including loading 

estimates, it is imperative to have continuous, daily streamflow records to pair with water-quality samples. However, 

this requirement presents a significant challenge in the study 

area where backwater conditions and technology limited 

gaging ability prior to the early 2000s at some critical sites 

(that is, CDR near Harrison, the St. Joe River at Ramsdell, 

and the Spokane River below lake outlet), at gaging sites that 

have been intermittently operated (that is, Pine, Ninemile, 

and Canyon Creeks), and at some important, long-term 

water-quality sites that have simply not had continuous gages 

(SFCDR at Kellogg and SFCDR at Smelterville). Depending 

on the site, different solutions were employed to create or 

extend streamflow records (table 1). In the St. Joe River at 

Ramsdell, the length of the gaging record simply limited the 

timespan available for water-quality analysis, and long-term 

streamflow analysis was completed using two upstream gages 

(St. Joe River at Calder and St. Maries River near Santa). 

In the Spokane River, a downstream gage (12419000) was 

directly used for long-term streamflow analysis and for extension of the continuous streamflow record of water-quality 

loading and trend analysis; this approach is consistent with 

previous loading analyses (Donato, 2006). For the CDR near 

Harrison, this report used a previously generated daily streamflow record for WYs 1991–2004. The record was developed 

using the USGS streamflow model FourPt (Donato, 2006). 

The FourPt model uses channel geometry and water-stage data 

at upstream (CDR near Cataldo) and downstream (lake stage 

at the Coeur d’Alene Lake outlet) sites to produce streamflows 

(Donato, 2006).

Finally, synthetic hydrographs were generated for some 

sites that had gaps in their records (Ninemile and Canyon 

Creeks), where streamgaging was discontinued but waterquality sample collection was not (Pine Creek), or where there 

was no gage but there was long-term water-quality sampling 

(SFCDR at Kellogg and SFCDR at Smelterville). In each 

case, the synthetic hydrograph was generated for the minimum 

amount of time necessary (for example, just for the record 

gap). Synthetic hydrographs use the relationship between daily 

streamflow at a continuous site and either daily streamflow 

or miscellaneous streamflow measurements (or estimates as 

described earlier) at a site with partial records or no gage, 

respectively, to generate a continuous streamflow record 

at the ungaged site (Hirsch, 1982; Nielsen, 1999; Granato, 

2009). The MOVE.1 regression technique was used on logtransformed data, with the Duan smoothing method to biascorrect the transformed synthetic hydrograph data (Granato, 

2009). The MOVE.1 technique was used to remedy the problem that the extended parts of streamflow records will have a 

loss of variance compared to a real record. The MOVE.1 compensates for this loss of variance. For Ninemile and Canyon 

Creeks, the nearest downstream site (SFCDR at Elizabeth 

Park) was used to generate the synthetic hydrographs. For 

the SFCDR at Kellogg and Smelterville, the nearest upstream 

continuous streamgaging site (SFCDR at Elizabeth Park) was 

used to generate the synthetic hydrographs. This is the closest, 

most reliable, and longest operating continuous streamgage 

for each of these sites. For Pine Creek, the nearest upstream 

site (East Fork Pine Creek) was used to generate the synthetic 

hydrograph (table 1).

Water-Quality Data for Water Years 1990–2003

A synopsis of data collected under various programs 

and cooperators in the 1990s is provided in Beckwith (1998). 

Specific methods for data collected in calendar years 1991–92 

are documented in Woods and Beckwith (1997); these data 

were collected as part of an effort to evaluate Coeur d’Alene 

Lake, including its nutrient and trace metal balances. Specific 

methods for data collected in WYs 1993–94 are documented 

in Beckwith and others (1997); these data were associated 

with a Natural Resources Damage Assessment. Data collection 

was coordinated with the EPA for the Remedial Investigation/

Feasibility Study beginning in WY 1996 (Beckwith, 1998). 

Additional data were collected under a separate but temporally 

and geographically overlapping USGS national water-quality 

program from WY 1997 to 2001 (Clark, 2003).

As described by Donato (2006), these studies differed in 

objectives, and, therefore, the number of samples collected 

and constituents analyzed also varied. Nonetheless, the studies 

similarly sought to collect samples over a range of hydrological conditions, and all samples were collected and analyzed by 

USGS personnel under standard, published methods that were 

current at the time of collection. Width and depth-integrated 

sampling procedures were used to collect samples pre-2004 

(Edwards and Glysson, 1988; Edwards and Glysson, 1999) 
Methods 11

except for during some extreme floods (Beckwith, 1996) and 

under some low-streamflow, backwatered conditions in the 

CDR when velocities were insufficient to use isokinetic samplers (Beckwith and others, 1997). Samples were composited, 

filtered, and preserved as appropriate and shipped to the USGS 

National Water-Quality Laboratory (Colorado) for analysis. 

Analytical and quality control and quality assurance procedures for this time period are documented in Fishman (1993)

and Pritt and Raese (1995), respectively.

One especially consequential change in sample collection and equipment cleaning procedures was implemented in 

WY 1994. Following a period of extensive testing, the USGS 

adopted parts per billion sampling and equipment cleaning 

protocols effective at the start of WY 1994 (U.S. Geological 

Survey, 1993). Water-quality samples with low levels of trace 

metals collected prior to this date have an unquantifiable risk 

of contamination; as such, data collected before this date at 

low concentrations should be reviewed carefully for inclusion 

in analyses (U.S. Geological Survey, 1992). The impact of this 

change on data quality and the data used for analyses hereinafter is discussed in the “Quality Control Samples” section.

Water-Quality Data for Water Years 2004–18

The surface water Basin Environmental Monitoring 

Program was implemented in WY 2004 and is ongoing as of 

2020; analyses for this report include data through WY 2018. 

Even within the program, sampling locations and frequencies 

have changed over time as described by Clark and Mebane 

(2014); during WYs 2009–18, up to 20 sites were sampled 

consistently multiple times per year. As with the older data, 

samples were taken over a range of hydrological conditions, 

were collected with width- and depth-integrating equipment 

and were then composited and subsampled (U.S. Geological 

Survey, variously dated). Samples for whole-water recoverable 

analyses (hereinafter referred to as “total”) were preserved as 

appropriate; samples for “dissolved” analyses were pumped 

through a 0.45 micrometer filter, then preserved as appropriate (U.S. Geological Survey, variously dated). Samples 

were shipped to the USGS Cascades Volcanic Observatory 

Laboratory (Washington State) for suspended sediment 

concentration and sand break analyses and sent to the USGS 

National Water-Quality Laboratory (Colorado) for all other 

analyses, including nutrients, trace metals, major cations, and 

anions (Garbarino and others, 2006).

Analyses

The goal of this report is to describe trends in concentrations and loads in the Spokane River watershed resulting 

from remedial activities. The drastically different lengths 

of water-quality records, and the fact that some important 

water-quality monitoring sites do not have associated gaging 

sites, necessitated the use of different approaches for analysis. 

Thus, streamflow trends were explored at a limited number of 

key gaging sites (6) in the study area. Because concentration 

data, but not necessarily continuous streamflow, were readily 

available for each of the WYs 2009–18 water-quality monitoring sites (20), ambient water-quality criteria (AWQC) ratios 

were used to describe change in concentrations throughout 

study area. For sites with 13–29 years of water-quality records 

and concurrent daily streamflow (12), annual mean concentrations and annual total loads and flow-normalized annual mean 

concentrations and annual total loads were estimated, and 

concentration and load trends analyses were completed. These 

analysis methods are described in greater detail below.

Ambient Water-Quality Criteria

For the constituents of concern, the water-quality criteria 

that are most broadly relevant across the study area for surface 

water are the AWQC. As used here, “AWQC” refers to the 

chronic criteria for aquatic life and vary across the study 

area. For surface waters in the SFCDR watershed (including 

tributaries), there are SFCDR-specific criteria defined in the 

Idaho Code. For all other waters in the study area (NFCDR, 

main-stem CDR, St. Joe River at Ramsdelland, Spokane River 

below lake outlets), the statewide Idaho criteria apply (Idaho 

Department of Environmental Quality, variously dated). Both 

the statewide and SFCDR-specific criteria for lead, zinc, 

and cadmium are expressed as equations that are hardnessdependent and thus vary by site and even by sampling event, 

as hardness typically varies with streamflow. As an example, a 

selection of AWQC under SFCDR and state-wide criteria for 

different hardnesses is shown in table 2.

In practice, accurate comparison to the regulatory criteria 

required that a unique AWQC was calculated for each site 

for each sampling event according to the criteria equations 

given in the Idaho Code (Idaho Department of Environmental 

Quality, variously dated). Thus, for the purpose of comparing site concentrations to AWQC across the study area, this 

report uses AWQC ratios. That is, the constituent concentration at each site during each sampling event was divided by 

the site- and event-specific AWQC to produce an AWQC ratio. 

An AWQC ratio greater than 1.0 indicates criteria exceedance, and an AWQC ratio less than or equal to 1.0 indicates 

that the water meets criteria. This convention is not unique to 

this report; it was also used by Clark and Mebane (2014) and 

throughout various Records of Decision (U.S. Environmental 

Protection Agency, 2002; 2012b), including for the purpose 

of defining some remedial action targets. The use of the 

word “exceedance” in the present report is as it is used in the 

Records of Decision–to evaluate remediation effectiveness. 

This usage differs from the explicit language in the Idaho 

Code, which defines compliance with chronic aquatic life 

criteria as a three-part definition such that the criteria concentration should not be exceeded for a 4-day average concentration more than once every 3 years (Idaho Department 

of Environmental Quality, variously dated). The sampling 

protocols used to collect the samples analyzed in this report 

did not include the collection of multiple samples within 
12 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

4-day periods at each site to meet the letter of the Idaho Code, 

which would have been logistically and financially infeasible. Instead, as chronic criteria concentrations are intended 

to protect aquatic communities from continuous exposure to 

chemicals, the chronic concentration values are simply considered the most appropriate benchmark for evaluating remedial 

progress.

Streamflow Trends

The WRTDS method relies on daily discharge to estimate daily concentrations and loads. While the original model 

allows the relationship between discharge and concentration 

to be flexible over time, the underlying assumption is that the 

discharge distribution over the studied time period remains 

the same (Hirsch and others, 2010). This assumption is not 

always appropriate, and a WRTDS extension provides a 

method to accommodate discharge changes over the period 

of record (Hirsch and DeCicco, 2018; Choquette and others, 2019). Thus, before beginning the WRTDS analysis, six 

key continuous gaging sites in the study area (SFCDR near 

Pinehurst, NFCDR at Enaville, CDR near Cataldo, St. Joe 

River at Calder, St. Maries River at Santa, and Spokane River 

near Post Falls) were analyzed for trends in streamflow from 

WY 1990 to 2018. The flowTrends R code, an extension of the 

EGRET package, was used to evaluate trends (Hirsch, 2018). 

Basic statistics such as daily discharge minimum, maximum, 

and median were compiled, and the non-parametric MannKendall trend test with Theil-Sen slope (Helsel and Hirsch, 

2002) was conducted to determine if there were statistically 

significant changes in any of these metrics over the 29-year 

period considered. The Mann-Kendall test determines whether 

a trend in discharge is statistically significant over time and 

is robust for non-normal data and against outliers, both of 

which are common in hydrologic data. The Theil-Sen slope 

provides an estimate of the direction and magnitude of the 

Mann-Kendall trend (Helsel and others, 2020). Additionally, 

the flowTrends code was used to create a visualization (called 

the Quantile-Kendall plot) of the Mann-Kendall trend test with 

Theil-Sen slope for each daily discharge statistic, starting with 

the minimum and moving to the second lowest daily discharge, the third lowest daily discharge, and so on through the 

maximum (Hirsch, 2018; Choquette and others, 2019).

Water Quality: Concentrations, Loads, and 

Trends

As described in the “Introduction” section, this report 

uses the WRTDS model and various extensions to describe 

concentrations and loads and trends in both over time. 

Specifically, WRTDS was used to estimate annual flownormalized concentrations and loads, whereas WRTDS_K was 

used to estimate annual mean concentrations and loads. The 

basic form of the underlying WRTDS model is:

ln(c) = β0 + β1 t + β2 ln(Q) +

 β3 sin(2πt) + β4 cos(2πt) + ε (1)

where

c is concentration;

Q is discharge;

t is time in years; and

ε is unexplained variation.

The equation is essentially a weighted regression model, 

and functionally is fit in the form of weighted Tobit model 

(also known as a “survival regression”). This form accommodates censored data because each concentration value can 

be expressed as a single number for uncensored data or as 

an interval (that is, between 0 and 0.5) in the case of censored data (Hirsch and others, 2015; Hirsch and De Cicco, 

2015). The method is implemented in R (R Core Team, 2019) 

using the EGRET package (Hirsch and De Cicco, 2015). The 

WRTDS_K enhancement is currently available as additional 

code (Hirsch, 2019).

As described previously in the “Data Collection” section, 

each site varies somewhat in the length of record, number 

of samples, and constituents available. Overall, 12 sites had 

enough data to implement the WRTDS modeling (Ninemile 

Creek; Canyon Creek; Pine Creek; SFCDR at Elizabeth Park, 

Table 2. Example ambient water-quality criteria for different sample hardness, South Fork Coeur d’Alene River-specific and Idaho 

state-wide criteria.

[Abbreviations: mg/L as CaCO3, milligram per liter as calcium carbonate; SFCDR, South Fork Coeur d'Alene River; μg/L, microgram per liter.]

Hardness 

(mg/L as 

CaCO3)

SFCDR ambient water-quality criteria Idaho statewide ambient water-quality criteria

Dissolved cadmium (μg/L)Dissolved lead 

(μg/L)

Dissolved zinc 

(μg/L)

Dissolved cadmium (μg/L)Dissolved lead 

(μg/L)

Dissolved zinc 

(μg/L)

10 0.19 3.3 42 0.15 0.54 37

25 0.37 7.7 78 0.25 0.54 37

35 0.47 11 97 0.31 0.79 49

50 0.62 15 123 0.38 1.2 66

100 1.0 28 195 0.57 2.5 118
Methods 13

at Kellogg, at Smelterville and near Pinehurst; NFCDR at 

Enaville; CDR near Cataldo and near Harrison; St. Joe River 

at Ramsdell; and Spokane River below lake outlet). Nine 

parameters (total and dissolved zinc, cadmium, and lead; 

total phosphorus and nitrogen; and orthophosphate) were 

considered, though not all parameters were modeled for all 

sites. Table 3 summarizes the sites, parameters, start and end 

dates, the number of samples (total and censored), and the flux 

bias statistic for each model (Hirsch, 2014). Generally, the 

longest records (25–29 years) were available for SFCDR near 

Pinehurst, CDR near Harrison, CDR near Cataldo, NFCDR 

at Enaville, and SFCDR at Elizabeth Park. Shorter intervals 

(17–23 years) were available for the tributaries and most 

other SFCDR sites. The shortest available records were for 

the SFCDR at Kellogg, the St. Joe River at Ramsdell and the 

Spokane River below lake outlet (13–16 years).

To develop a specific WRTDS model, each parameter at 

each site needed to have at least 60 samples, with a minimum 

of 40 uncensored results at this minimum threshold. Most sites 

and parameters had at least 100 samples, with 50 percent or 

more uncensored results. WRTDS models were developed for 

most metals at most sites, but nutrient models were generally 

limited to shorter time periods and downstream sites which 

had fewer censored values (table 3).

For each model, the flux bias statistic was computed from 

the results. Essentially, this statistic compares the difference 

between the sum of the estimated fluxes (that is, loads) on the 

sampled days to the sum of the true (sampled) fluxes on the 

sampled days (Sprague and others, 2011; Hirsch, 2014). The 

flux bias is calculated as:

Flux bias = (

∑i=1 n Lp,i −∑i=1 n ___________ Lo,i

∑i=1 n Lo,i

 ) × 100 (2)

where

Lp,i is the predicted flux from WRTDS for day i;

Lo,i is the observed flux for day i; and

n is the number of sampled days in the 

monitoring record.

Values near zero indicate an unbiased model, negative 

values indicate negative bias (that is, a model that underpredicts flux), and positive values indicate positive bias (that is, 

a model that overpredicts flux). Previous work has found that 

a flux bias statistic of -0.1 to 0.1 generally corresponds to true 

bias of approximately plus or minus 10 percent. However, the 

relationship between the flux bias statistic and the true bias 

was highly nonlinear, with statistic values near 0.6 having true 

bias in the range of 100–125 percent (Hirsch, 2014)

Functionally, WRTDS creates concentration and load 

estimates for every day within the period of study. These 

estimates are then averaged over the time period of interest (in this report, each water year) to produce annual means 

(Hirsch and others, 2010). Additionally, the EGRET package 

contains a procedure to estimate flow-normalized concentrations and loads. This procedure uses the underlying discharge 

data for each day (that is, September 1) to create a probability 

density function of discharge values. Then the integral of 

each estimated concentration for each discharge on that day 

is integrated over the discharge probability density function, 

and so on for every day of the study period. This function is 

described:

E[Cfn(T)

]

=∫0

∞

w(Q,T)∙ fTs(Q)dQ (3)

where

is the flow-normalized concentration for time 

T (a specific day of a specific year);

w(Q,T) is the WRTDS estimate of concentration as a 

function of Q (discharge) and T (time, in 

years); and

fTs(Q) is the probability density function of 

discharge, specific to a particular time of 

year, designated as Ts.

Functionally, the flow-normalized concentrations for a 

particular day of a particular year was based on the relationship of concentration to discharge for that day of that year 

and on the probability distribution of discharge for that day 

of the year (using the flow record from all years) (Hirsch 

and others, 2010; Hirsch and De Cicco, 2015). Similarly, the 

flow-normalized load used this same relationship of concentration to discharge, but the concentrations were multiplied by 

discharge to represent load.

The flow-normalized concentrations and loads were 

then used to calculate trends for net change for the full 

period of record (which varies by site and constituent) and 

for change from WY 2009 to 2018. These calculations are 

relatively simple:

Net c hange c c

t t 2 1

= − (4)

Net change in percent =

c

t 2

− c

t 1

c

t 1

⎛

⎝

⎜ ⎞

⎠

⎟ × 100 (5)

where

ct1 is the annual mean flow-normalized 

concentration in year t1; and

ct2 is the annual mean flow-normalized 

concentration in year t2.

These calculations were originally described in Sprague 

and others (2011). Trends for loads are computed in the same 

way, simply using the flow-normalized annual mean load in 

place of the flow-normalized annual mean concentrations.
14 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

Table 3. Summary of site, parameters, water years, and samples used for Weighted Regressions on Time, Discharge and Season 

(WRTDS) and WRTDS with Kalman filtering (WRTDS_K) models, and flux bias statistics for WRTDS models, water years 1990–2018.

[Abbreviations: CDR, Coeur d'Alene River; NFCDR, North Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River]

Site name (short, as used in this 

report) Constituent

Water year Number of 

water years

Number 

of total 

samples

Number of 

censored 

samples

Flux bias 

statistic Start End

NFCDR at Enaville Dissolved cadmium 2001 2018 18 113 52 0.05

NFCDR at Enaville Dissolved lead 2001 2018 18 106 15 -0.16

NFCDR at Enaville Dissolved zinc 1997 2018 22 154 17 -0.13

NFCDR at Enaville Total cadmium 2001 2018 18 114 56 -0.09

NFCDR at Enaville Total lead 1994 2018 25 171 55 0.03

NFCDR at Enaville Total nitrogen 2004 2018 15 80 32 -0.01

NFCDR at Enaville Total phosphorus 1998 2018 21 157 39 -0.16

NFCDR at Enaville Total zinc 1994 2018 25 170 39 -0.05

Canyon Creek Dissolved cadmium 1999 2018 20 112 0 -0.04

Canyon Creek Dissolved lead 1999 2018 20 112 0 -0.05

Canyon Creek Dissolved zinc 1999 2018 20 111 0 -0.04

Canyon Creek Total cadmium 1999 2018 20 108 0 -0.07

Canyon Creek Total lead 1999 2018 20 109 0 -1.45

Canyon Creek Total phosphorus 2002 2018 17 75 27 -0.97

Canyon Creek Total zinc 1999 2018 20 108 0 -0.06

Ninemile Creek Dissolved cadmium 1999 2018 20 100 0 -0.02

Ninemile Creek Dissolved lead 1999 2018 20 100 0 -0.01

Ninemile Creek Dissolved zinc 1999 2018 20 100 0 -0.02

Ninemile Creek Total cadmium 1999 2018 20 94 0 -0.06

Ninemile Creek Total lead 1999 2018 20 95 0 -0.67

Ninemile Creek Total zinc 1999 2018 20 93 0 -0.06

SFCDR at Elizabeth Park Dissolved cadmium 1997 2018 22 138 0 0.00

SFCDR at Elizabeth Park Dissolved lead 1997 2018 22 138 0 -0.03

SFCDR at Elizabeth Park Dissolved zinc 1997 2018 22 139 0 -0.01

SFCDR at Elizabeth Park Total cadmium 1993 2018 26 166 0 -0.14

SFCDR at Elizabeth Park Total lead 1993 2018 26 167 0 -0.06

SFCDR at Elizabeth Park Total nitrogen 2004 2018 15 81 4 -0.23

SFCDR at Elizabeth Park Total phosphorus 2002 2018 17 87 22 -0.64

SFCDR at Elizabeth Park Total zinc 1993 2018 26 167 0 -0.15

SFCDR at Kellogg Dissolved cadmium 2006 2018 13 65 0 0.00

SFCDR at Kellogg Dissolved lead 2006 2018 13 65 0 -0.27

SFCDR at Kellogg Dissolved zinc 2006 2018 13 65 0 0.00

SFCDR at Kellogg Total cadmium 2006 2018 13 65 0 -0.15

SFCDR at Kellogg Total lead 2006 2018 13 65 0 -0.51

SFCDR at Kellogg Total nitrogen 2006 2018 13 65 4 -0.23

SFCDR at Kellogg Total phosphorus 2006 2018 13 65 19 -0.61

SFCDR at Kellogg Total zinc 2006 2018 13 65 0 -0.15

SFCDR at Smelterville Dissolved cadmium 2002 2018 17 98 0 -0.01

SFCDR at Smelterville Dissolved lead 2002 2018 17 98 0 -0.12

SFCDR at Smelterville Dissolved zinc 2002 2018 17 98 0 -0.01

SFCDR at Smelterville Total cadmium 2002 2018 17 97 0 -0.09
Methods 15

Table 3. Summary of site, parameters, water years, and samples used for Weighted Regressions on Time, Discharge and Season 

(WRTDS) and WRTDS with Kalman filtering (WRTDS_K) models, and flux bias statistics for WRTDS models, water years 1990–2018.—

Continued

[Abbreviations: CDR, Coeur d'Alene River; NFCDR, North Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River]

Site name (short, as used in this 

report) Constituent

Water year Number of 

water years

Number 

of total 

samples

Number of 

censored 

samples

Flux bias 

statistic Start End

SFCDR at Smelterville Total lead 2002 2018 17 98 0 -0.85

SFCDR at Smelterville Total nitrogen 2004 2018 15 83 6 -0.15

SFCDR at Smelterville Total phosphorus 2002 2018 17 85 1 -0.37

SFCDR at Smelterville Total zinc 2002 2018 17 97 0 -0.11

Pine Creek Dissolved zinc 1999 2018 20 76 0 -0.03

Pine Creek Total cadmium 1999 2018 20 62 9 -0.15

Pine Creek Total lead 1999 2018 20 66 18 -0.62

Pine Creek Total zinc 1999 2018 20 76 0 -0.10

SFCDR near Pinehurst Dissolved cadmium 1990 2018 29 194 0 -0.01

SFCDR near Pinehurst Dissolved lead 1990 2018 29 191 2 -0.04

SFCDR near Pinehurst Dissolved zinc 1990 2018 29 195 0 0.00

SFCDR near Pinehurst Orthophosphate 1990 2018 29 163 28 0.02

SFCDR near Pinehurst Total cadmium 1992 2018 27 201 0 -0.01

SFCDR near Pinehurst Total lead 1992 2018 27 205 1 0.12

SFCDR near Pinehurst Total nitrogen 2004 2018 15 81 1 -0.05

SFCDR near Pinehurst Total phosphorus 1990 2018 29 224 11 -0.11

SFCDR near Pinehurst Total zinc 1992 2018 27 205 1 0.03

CDR near Cataldo Dissolved cadmium 1990 2018 29 101 6 0.00

CDR near Cataldo Dissolved lead 1990 2018 29 101 11 -0.35

CDR near Cataldo Dissolved zinc 1990 2018 29 103 0 0.02

CDR near Harrison Dissolved cadmium 1996 2018 23 150 5 -0.02

CDR near Harrison Dissolved lead 1996 2018 23 150 2 -0.33

CDR near Harrison Dissolved zinc 1996 2018 23 152 0 -0.06

CDR near Harrison Orthophosphate 1999 2018 20 116 57 0.00

CDR near Harrison Total cadmium 1991 2018 28 236 2 -0.15

CDR near Harrison Total lead 1991 2018 28 249 0 -0.07

CDR near Harrison Total nitrogen 2003 2018 16 92 10 -0.03

CDR near Harrison Total phosphorus 1999 2018 20 131 2 -0.28

CDR near Harrison Total zinc 1991 2018 28 237 1 -0.14

St. Joe River at Ramsdell Dissolved lead 2005 2018 14 86 13 -0.03

St. Joe River at Ramsdell Dissolved zinc 2005 2018 14 88 31 -0.11

St. Joe River at Ramsdell Orthophosphate 2005 2018 14 88 31 0.01

St. Joe River at Ramsdell Total lead 2005 2018 14 88 1 -0.17

St. Joe River at Ramsdell Total nitrogen 2005 2018 14 87 5 -0.06

St. Joe River at Ramsdell Total phosphorus 2005 2018 14 88 0 -0.18

St. Joe River at Ramsdell Total zinc 2005 2018 14 88 46 -0.08

Spokane River below lake outlet Dissolved cadmium 2003 2018 16 98 1 0.00

Spokane River below lake outlet Dissolved lead 2003 2018 16 98 0 -0.18

Spokane River below lake outlet Dissolved zinc 2003 2018 16 98 0 -0.02

Spokane River below lake outlet Total cadmium 2003 2018 16 98 0 -0.01
16 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

In addition to calculating trends, the EGRETci (De Cicco 

and others, 2019) package was used to estimate the uncertainty 

associated with these trends. This package uses a block bootstrapping method to construct confidence intervals around a 

given trend. Essentially, by randomly subsampling the dataset 

and recreating the WRTDS model over multiple iterations, the 

method calculates the trend many times (Hirsch and others, 

2015). These bootstrap outcomes can be used in a variety 

of ways, but in this report these outcomes are summarized 

to describe the likelihood of the trend in common language 

(Hirsch and others, 2015; Oelsner and others, 2017). For 

example, if out of 100 bootstrap replicates, 85 or more indicated an increasing trend, then the trend has a greater than or 

equal to 85 percent chance of being truly up and is described 

as “likely up.” If out of the 100 bootstrap replicates, 15 or 

fewer indicated an increasing trend, the trend has a greater 

than or equal to 85 percent chance of being truly down and 

is described as “likely down.” This report uses the descriptor conventions established by Oelsner and others (2017)

and shown in table 4. For each model and trend interval, the 

minimum number of bootstrap replicates was set at 39 and 

the maximum number of bootstrap replicates was set at 100 

to balance statistical confidence with computational demand, 

and the block length was set at 200 based on the sampling 

intervals in the underlying dataset (Hirsch and others, 2015). 

The bootstrap replicate outcomes were also used to construct 

90 percent confidence intervals for the trend slopes and to 

describe the median trend slope for select sites and constituents. Because these replicates were run for only a few models, 

the minimum and maximum number of replicates was set 

higher (500) to achieve higher statistical confidence.

Results

Streamflow Stationarity

Trends in streamflow were explored at six key gaging sites (SFCDR near Pinehurst, NFCDR at Enaville, CDR 

near Cataldo, St. Joe River at Calder, St. Maries River near 

Santa, and Spokane River near Post Falls). The latter three 

gaging sites differ from the sites used for water-quality 

analyses (table 1). For long-term streamflow analysis (WYs 

1990–2018), gaging sites with complete streamflow records 

that were as close as possible to water-quality sites were 

selected. A variety of streamflow statistics (WY minimum, 

median, and maximum daily streamflows) were tested for significant trends over the period of record. Except for increasing 

minimum streamflows in the Spokane River near Post Falls, 

there were no significant trends in the tested statistics over the 

period of record. At the Spokane River near Post Falls site, 

this trend was likely the result of changes to hydroelectric dam 

operations that control streamflow at this site

The overall lack of statistical significance in streamflow 

trends is shown in Quantile-Kendall plots in figure 2. For 

each site, the results of a Mann-Kendall test with the TheilSen slope is shown for each ranked streamflow (calculated 

by water year). Some of the lowest streamflows in the St. 

Joe River at Calder modestly but significantly decreased 

(fig. 2d), and minimum streamflows in the Spokane River near 

Post Falls increased while flows in the 10th–25th percentile 

decreased (fig. 2f). Generally, however, across most streamflows at most sites, calculated trends were modest, ranging 

from -1.5 percent per year decreases to about 1.5 percent per 

year increases, and the vast majority of these trends were not 

Table 3. Summary of site, parameters, water years, and samples used for Weighted Regressions on Time, Discharge and Season 

(WRTDS) and WRTDS with Kalman filtering (WRTDS_K) models, and flux bias statistics for WRTDS models, water years 1990–2018.—

Continued

[Abbreviations: CDR, Coeur d'Alene River; NFCDR, North Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River]

Site name (short, as used in this 

report) Constituent

Water year Number of 

water years

Number 

of total 

samples

Number of 

censored 

samples

Flux bias 

statistic Start End

Spokane River below lake outlet Total lead 2003 2018 16 98 0 -0.40

Spokane River below lake outlet Total nitrogen 2004 2018 15 91 8 0.01

Spokane River below lake outlet Total phosphorus 2003 2018 16 98 17 0.00

Spokane River below lake outlet Total zinc 2003 2018 16 98 0 -0.01

Table 4. Statistical likelihood descriptors.

[Numeric range of the statistical likelihood specifically refers to the likelihood 

that a trend is up. Range and descriptors from Oelsner and others (2017). 

Symbols: ≥, greater than or equal to; ≤, less than or equal to; <, less than; >, 

greater than]

Range of statistical likelihood Descriptor

≥0.85 to ≤1.0 Likely up

≥0.70 to <0.85 Somewhat likely up

>0.30 to <0.70 About as likely as not

>0.15 to ≤0.30 Somewhat likely down

≥0 to ≤0.15 Likely down
Results 17

significant at p ≤ 0.10. One thing that all six sites had in common was that median streamflows tended to decrease with a 

slope of about -1.5 percent per year, but these decreases were 

not statistically significant. Also, the high flows (generally 

those above the 90th percentile) all tended to show modest 

increases (0.5–1.0 percent per year), but they were almost 

never significant.

These results suggest that streamflows in the study area 

were reasonably stationary over the period of water-quality 

analysis (WYs 1990–2018). This does not imply that important changes in streamflow are not occurring in the Spokane 

River watershed; for example, streamflows may be changing 

seasonally or over longer time periods. Furthermore, there 

may be important changes to streamflow occurring that are not 

Trend slope, in percent per year

C. Coeur d’Alene River near Cataldo

0.001 0.01 0.05 0.1 0.25 0.5 0.75 0.9 0.95 0.99 0.999

−2.0

−1.5

−1.0

−0.5

0.0

0.5

1.0

1.5

B. North Fork Coeur d’Alene River at Enaville

−2.0

−1.5

−1.0

−0.5

0.0

0.5

1.0

1.5

Daily non-exceedance probability

F. Spokane River near Post Falls

−2

−1

0

1

2

3

D. St. Joe River at Calder

−1.5

−1.0

−0.5

0.0

0.5

1.0

E. St. Maries River near Santa

−2.0

−1.5

−1.0

−0.5

0.0

0.5

1.0

A. South Fork Coeur d’Alene River near Pinehurst

−1.0

−0.5

0.0

0.5

1.0

1.5

p−value

EXPLANATION

>0.1 0.05 to 0.1 <0.05

0.001 0.01 0.05 0.1 0.25 0.5 0.75 0.9 0.95 0.99 0.999

0.001 0.01 0.05 0.1 0.25 0.5 0.75 0.9 0.95 0.99 0.999 0.001 0.01 0.05 0.1 0.25 0.5 0.75 0.9 0.95 0.99 0.999

0.001 0.01 0.05 0.1 0.25 0.5 0.75 0.9 0.95 0.99 0.999 0.001 0.01 0.05 0.1 0.25 0.5 0.75 0.9 0.95 0.99 0.999

Figure 2. Quantile-Kendall plots showing trends in streamflow for water years 1990–2018 for select sites in the Spokane River 

watershed, northern Idaho. Trend slope represents Theil-Sen slope expressed as percent per year. Probability value (p-value) 

represents the Mann-Kendall trend test results for each ranked streamflow. Site locations are shown in figure 1. Site descriptions 

are in table 1. Abbreviations: >, greater than; <, less than.
18 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

captured by the metrics used here. For example, this analysis 

did not consider the timing or duration of spring snowmelt 

runoff peaks, nor the frequency of rain-on-snow flooding 

events. However, for the purposes of this report, the lack 

of significant trends in most streamflows at most sites over 

the period of the water-quality record supported the use of 

WRTDS without the extension that accommodates for changing streamflows.

Quality Control Samples

For long-term trend analyses, particularly those that rely 

on data collected under multiple sampling programs as this 

report does, careful evaluation of the underlying data quality is critical for conferring confidence in the environmental 

reality of observed trends. Therefore, quality control samples 

collected from WY 1997 to 2018 were examined for each 

of the water-quality sites used in this report. There were no 

quality control samples collected, at least for the analytes 

considered here, from WY 1990 to 1996. Additionally, most 

of the blank and replicate samples were collected from WY 

2009 to 2018, which was the period sampled under the most 

recent protocols. As discussed in the “Methods” section, 

USGS sampling and cleaning procedures for low-level metals 

changed in WY 1994. Because of this change, and the lack of 

pertinent QC sample data from this period to fully evaluate the 

impact of this change, total and dissolved metal sample results 

in the NFCDR at Enaville collected prior to WY 1994 were 

removed from this analysis because sample contamination 

may have caused high metals bias in samples from this period. 

NFDCR at Enaville was the only site with both low metals 

concentrations and samples collected prior to WY 1994 and 

was therefore the only site affected by this potential source of 

contamination.

From WY 1997 to 2018, 95 blank samples were collected 

(table 5). Detections in the blanks for nutrients (total phosphorus and nitrogen and orthophosphate) and total and dissolved cadmium were rare (0–6 detections in 66–90 samples). 

Detections for total and dissolved zinc were low (13–14 

detections in 90–93 samples) and detected concentrations were 

low, particularly relative to ambient zinc concentrations in the 

study area (table 5).

Total and dissolved lead detections were most frequent, 

with 50–22 detections in 91 and 93 samples, respectively 

(table 5). Total lead detections occurred occasionally from WY 

1997 to 2018, and the median detection (0.12 microgram per 

liter [μg/L]) was generally near the detection limit. The maximum detection (8.53 μg/L) was more than 4 times higher than 

the next highest detected concentration and was collected in 

WY 1999 in a blank from Canyon Creek, a site with extremely 

high lead concentrations (the associated sample concentration 

was 2,000 μg/L). In an area where lead is pervasive and occurs 

at very high concentrations, the frequent blank detections 

reflect the challenge inherent in field decontamination of sampling equipment. To this end, field staff have adopted a project 

protocol of using only laboratory decontaminated equipment 

at sites with low metals concentrations (for example, SFCDR 

near Mullan, NFCDR at Enaville, St. Joe River at Ramsdell 

and Spokane River below lake outlet) to minimize total lead 

contamination at the most susceptible sites. Correspondingly, 

all blanks with total lead detections greater than 1.0 μg/L were 

associated with high concentration lead sites sampled with 

field decontaminated equipment, whereas blanks at low concentration lead sites either had non-detected lead or lead concentrations close to the detection limit (0.04 μg/L). The project 

protocol to manage sampling equipment has therefore successfully minimized lead contamination at the sites most susceptible to contamination bias, while the slightly higher concentration lead detections associated with field cleaned equipment 

were unlikely to affect data at the associated sites with much 

Table 5. Summary of blank sample results, water years 1997–2018.

[Results summarized from 95 blank samples collected from October 15, 1996, to September 17, 2018. Abbreviations: mg/L, milligram per liter; NA, not applicable; μg/L, microgram per liter. Symbols: ; < 0.004, sample concentration not detected at 0.004 mg/L.]

Constituent Units

Number 

of blank 

samples

Number of 

detections

Median concentration of detectionsMaximum concentration of detections

Minimum detection limit

Maximum 

detection 

limit

Total phosphorus mg/L 78 3 0.001 0.005 <0.004 <0.008

Orthophosphate mg/L 66 0 NA NA <0.001 <0.012

Total nitrogen mg/L 73 2 0.255 0.260 <0.05 <0.10

Dissolved cadmium μg/L 93 6 0.040 0.259 <0.016 <1.0

Total cadmium μg/L 90 6 0.039 0.101 <0.014 <1.0

Dissolved lead μg/L 93 22 0.074 4.82 <0.015 <1

Total lead μg/L 91 50 0.12 8.53 <0.04 <1.0

Dissolved zinc μg/L 93 14 1.7 12 <0.6 <20.0

Total zinc μg/L 90 13 2.4 6.0 <1 <10
Results 19

higher ambient lead concentrations. Therefore, despite more 

frequent than ideal detections, total lead data were of sufficient 

quality for inclusion in the analyses presented in this report.

In contrast to the total lead detections, dissolved lead 

detections were clustered in successive samples in WY 2011 

and WYs 2017–18. This pattern, along with relatively low 

total lead concentrations in the same blanks and anomalously 

high dissolved lead values with very low total lead values 

in regular samples at low-metal sites (SFCDR near Mullan, 

NFCDR at Enaville, St. Joe River at Ramsdell) during the 

same time, points to filter contamination as the cause of these 

detections (Mueller and others, 2015). There are known, documented filter contamination issues with cobalt and manganese 

that persist despite a 2-liter deionized water rinse of filters 

before introducing ambient waters (U.S. Geological Survey, 

2016a); it is therefore plausible, although presently not formally documented, that similar issues may occur in periodic 

filter batches for dissolved lead. Generally, dissolved lead 

blank concentrations were low relative to most site concentrations and these data were of sufficient quality for inclusion in 

the analyses presented in this report.

However, there were some samples for which filter 

contamination was more problematic. Increasing trends in 

dissolved lead over the period of record at low-metal sites 

(NFCDR at Enaville and St. Joe River at Ramsdell) were 

investigated carefully to understand the potential impact of 

filter contamination bias. Several anomalously high dissolved 

lead and dissolved cadmium concentrations at these sites and 

at SFCDR near Mullan in WYs 2017–18 were ultimately 

removed from the analysis because paired total lead and 

cadmium concentrations were very low, pointing to filter 

contamination problems. However, it was not possible with 

the available quality control data to determine whether filter 

contamination bias also affected much lower concentrations 

of dissolved lead or whether the increasing trends in dissolved lead concentrations reflect a real environmental trend. 

Thus, lower dissolved lead concentrations at low-metal sites 

may be affected by filter contamination bias, but the analyses 

presented in this report retained these data (and the trends 

following from them) to be as conservative as possible in the 

event that these trends indicate real environment change.

From WY 1997 to 2018, 102 split replicate samples were 

collected (table 6). Split replicate samples were collected by 

taking two samples from one churn, with identical processing of each. As such, results from these samples represent the 

effects of processing and analysis variability but minimize 

the effects of environmental and sampling variability. The 

median relative percent difference between replicate results 

for the eight constituents measured ranged from 0 to 4.8 

percent. All constituents had occasional occurrences of high 

relative percent differences, with maximums ranging from 40 

to 198 percent, but only 15 percent or fewer of samples for 

all constituents had relative percent differences greater than 

20 percent. For all constituents, the majority of replicates had 

relative percent differences less than 10 percent (table 6). 

Overall, no clear patterns in bigger or smaller relative percent 

differences were observed with time or constituents. Thus, 

the replicate results from WY 1997 to WY 2019 suggest that 

sample processing and analysis methods produced data of sufficient quality to be used in the analyses presented hereinafter.

Comparisons to Ambient Water-Quality Criteria

Generally, the range and median AWQC ratios for dissolved zinc have consistently decreased at most sites in the 

study area from the mid-1990s to WY 2018 based on simple 

visual comparison of boxplots (fig. 3; table 7). Nonetheless, 

the WYs 2014–18 AWQC ratios were well above 1.0 (that 

is, concentrations were above site-specific standards) at most 

sites, with median ratios ranging from 1.7 (Pine Creek) to 27 

(Seeps north of tailings; table 7). Several sites (SFCDR near 

Mullan, NFCDR at Enaville, and St. Joe River at Ramsdell) 

have been consistently below criteria during the period 

of record (fig. 3) except for two samples above criteria at 

NFCDR at Enaville during spring runoff events (fig. 3). In 

WYs 2014–18, median concentrations in the Spokane River 

Table 6. Summary of replicate sample results, water years 1997–2018.

[Results summarized from 102 replicate samples collected from April 17, 1997, to September 19, 2018. Symbols: >, greater than; <, less than]

Constituent Number of 

replicates

Median relative 

percent difference

Maximum relative 

percent difference

Number of replicates 

with relative percent 

difference >20 percent

Percentage of replicates with 

relative percent difference

<10 percent

Total phosphorus 69 3.8 40 7 50

Orthophosphate 38 0 100 11 26

Dissolved cadmium 79 2.0 198 14 32

Total cadmium 84 2.2 195 5 73

Dissolved lead 92 3.3 197 4 76

Total lead 97 4.8 191 15 69

Dissolved zinc 96 1.7 198 12 70

Total zinc 96 1.4 196 6 85
20 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

1990−19931994−1998

1999−2003

2004−2008

2009−2013

2014−2018

1990−1993

1994−1998

1999−20032004−2008

2009−2013

2014−2018

1990−1993

1994−19981999−2003

2004−20082009−2013

2014−2018

1990−19931994−1998

1999−20032004−2008

2009−2013

2014−2018

2.5

5.0

7.5

10.0

0

10

20

30

2

4

6

8

0.0

2.5

5.0

7.5

10.0

12.5

0.5

1.0

1.5

2.0

0

10

20

30

40

2

4

6

2.5

5.0

7.5

10.0

0.0

0.5

1.0

1.5

0.00

0.25

0.50

0.75

1.00

0

10

20

30

40

0

5

10

15

0

25

50

75

100

5

10

3

6

9

0.00

0.25

0.50

0.75

1.00

2.5

5.0

7.5

0

2

4

6

1

2

3

3

6

9

12

CDR at Rose Lake CDR near Harrison St. Joe River at Ramsdell Spokane River below lake outlet

Pine Creek SFCDR near Pinehurst NFCDR at Enaville CDR near Cataldo

Bunker Creek Government Gulch SFCDR at Smelterville SFCDR above Pine Creek

SFCDR at Elizabeth Park Milo Creek SFCDR at Kellogg Seeps north of tailings

SFCDR near Mullan Canyon Creek Ninemile Creek SFCDR at Wallace 

Ambient water quality criteria ratio for dissolved zinc

1.5 times the upper interquartile range

75th percentile

Median

25th percentile

1.5 times the lower interquartile range

Values beyond 1.5 times the interquartile range

Ambient water quality criteria ratio of 1

EXPLANATION

Figure 3. Dissolved zinc ambient water-quality criteria ratios for water years 1990–2018 for sites in the Spokane River watershed, 

northern Idaho. Site locations are shown in figure 1. Data were not available for all sites for all water years. Boxplots present as 

lines where the underlying data are limited to fewer than four samples. Abbreviations: CDR, Coeur d’Alene River; NFCDR, North 

Fork Coeur d’Alene River; SFCDR, South Fork Coeur d’Alene River.
Results 21

Table 7. Median ambient water-quality criteria ratios for dissolved cadmium, lead and zinc, water years 1990–2018, for sites in the 

Spokane River watershed, northern Idaho.

[Data were not available for all sites for all water years. Abbreviations: AWQC, ambient water-quality criteria; CDR, Coeur d'Alene River; NFCDR, North 

Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River; NA, not available]

Site name

(short, as used in this report)

Time 

interval 

(water years)

Number 

of total 

samples

Median AWQC ratio

Dissolved 

cadmium

Dissolved

lead

Dissolved

zinc

NFCDR at Enaville 1994–98 13 NA NA 0.2

NFCDR at Enaville 1999–2003 61 0.1 0.2 0.1

NFCDR at Enaville 2004–08 36 0.2 0.2 0.1

NFCDR at Enaville 2009–13 23 0.1 0.2 0.1

NFCDR at Enaville 2014–18 18 0.2 0.2 0.1

SFCDR near Mullan 1999–2003 21 NA 0.1 0.1

SFCDR near Mullan 2004–08 11 0.1 0.0 0.1

SFCDR near Mullan 2009–13 9 0.1 0.0 0.1

SFCDR near Mullan 2014–18 10 0.1 0.0 0.1

Canyon Creek 1999–2003 42 28 2 19

Canyon Creek 2004–08 25 22 1.1 16

Canyon Creek 2009–13 23 20 1.4 15

Canyon Creek 2014–18 21 15 1.2 11

Ninemile Creek 1999–2003 44 24 1.7 20

Ninemile Creek 2004–08 11 24 1.1 17

Ninemile Creek 2009–13 24 23 1.4 17

Ninemile Creek 2014–18 21 19 1.3 16

SFCDR at Wallace 1999–2003 1 7.3 1.3 4.6

SFCDR at Wallace 2009–13 15 6.6 0.4 5.6

SFCDR at Wallace 2014–18 20 5.2 0.3 4.2

SFCDR at Elizabeth Park 1994–98 14 8.7 0.4 5.8

SFCDR at Elizabeth Park 1999–2003 44 8.7 0.3 6.2

SFCDR at Elizabeth Park 2004–08 37 6.7 0.2 5.2

SFCDR at Elizabeth Park 2009–13 23 5.4 0.2 4

SFCDR at Elizabeth Park 2014–18 21 5.1 0.1 3.9

SFCDR at Kellogg 1999–2003 4 8.6 0.5 5.2

SFCDR at Kellogg 2004–08 20 6.5 0.3 5

SFCDR at Kellogg 2009–13 23 5.6 0.3 4.4

SFCDR at Kellogg 2014–18 21 5.2 0.2 3.9

Government Gulch 1999–2003 18 390 0.6 62

Government Gulch 2009–13 1 120 0.2 22

Government Gulch 2014–18 10 94 0.5 19

SFCDR at Smelterville 1999–2003 15 9 0.3 6.1

SFCDR at Smelterville 2004–08 37 7.5 0.2 5.4

SFCDR at Smelterville 2009–13 23 7.5 0.2 5

SFCDR at Smelterville 2014–18 24 6.6 0.2 4.5

SFCDR above Pine Creek 2009–13 23 7.5 0.2 5.4

SFCDR above Pine Creek 2014–18 21 6 0.2 4.6

Pine Creek 1999–2003 45 1.8 0.1 2.2

Pine Creek 2004–08 11 1.4 0.1 1.9
22 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

Table 7. Median ambient water-quality criteria ratios for dissolved cadmium, lead and zinc, water years 1990–2018, for sites in the 

Spokane River watershed, northern Idaho.—Continued

[Data were unavailable for all sites for all water years. Abbreviations: AWQC, ambient water-quality criteria; CDR, Coeur d'Alene River; NFCDR, North 

Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River; NA, not available]

Site name (short, as used in this report)

Time 

interval 

(water years)

Number 

of total 

samples

Median AWQC ratio

Dissolved 

cadmium

Dissolved

lead

Dissolved

zinc

Pine Creek 2009–13 9 1.4 0.1 1.7

Pine Creek 2014–18 11 1.2 0.1 1.7

SFCDR near Pinehurst 1990–93 14 12 0.2 9.1

SFCDR near Pinehurst 1994–98 24 9.3 0.3 9

SFCDR near Pinehurst 1999–2003 74 8 0.3 6.6

SFCDR near Pinehurst 2004–08 37 6.7 0.2 5.3

SFCDR near Pinehurst 2009–13 23 6.1 0.2 4.5

SFCDR near Pinehurst 2014–18 21 5.1 0.2 4

CDR near Cataldo 1990–93 13 8.7 4.3 9.1

CDR near Cataldo 1994–98 14 7.9 1.8 7.2

CDR near Cataldo 1999–2003 22 6.5 1.9 6.7

CDR near Cataldo 2004–08 11 5.4 1.8 5.9

CDR near Cataldo 2009–13 17 3.2 1.2 3.4

CDR near Cataldo 2014–18 22 3.1 1.5 3.2

CDR at Rose Lake 1994–98 16 7.1 4.9 6.8

CDR at Rose Lake 1999–2003 16 6.3 3.9 6.4

CDR at Rose Lake 2014–18 17 3.1 3.5 3.3

CDR near Harrison 1994–98 18 6.3 11 7.3

CDR near Harrison 1999–2003 39 5.1 8.1 5.5

CDR near Harrison 2004–08 40 3.5 7.2 4.3

CDR near Harrison 2009–13 29 3.6 12 4.3

CDR near Harrison 2014–18 24 2.9 8.3 3.2

St. Joe River at Ramsdell 1999–2003 5 0.1 0.2 0.0

St. Joe River at Ramsdell 2004–08 36 0.2 0.1 0.0

St. Joe River at Ramsdell 2009–13 30 0.1 0.1 0.1

St. Joe River at Ramsdell 2014–18 22 0.2 0.2 0.1

Spokane River below lake outlet 1999–2003 7 1.0 0.4 1.4

Spokane River below lake outlet 2004–08 38 0.8 0.4 1.3

Spokane River below lake outlet 2009–13 30 0.8 0.3 1.5

Spokane River below lake outlet 2014–18 23 0.7 0.4 1.0

Milo Creek 1999–2003 2 6.9 8.9 4.4

Milo Creek 2009–13 1 5.6 11 6.8

Milo Creek 2014–18 10 6.1 11 6.3

Bunker Creek 1999–2003 1 0.8 NA 0.3

Bunker Creek 2009–13 1 3.6 0.0 1.3

Bunker Creek 2014–18 13 4.1 0.0 2.7

Seeps north of tailings 2009–13 1 57 0.0 37

Seeps north of tailings 2014–18 10 22 0.0 27
Results 23

below lake outlet met criteria for the first time in the period of 

record (fig. 3). Apparent increases in dissolved zinc AWQC 

ratios at a few sites (SFCDR at Wallace, Milo Creek and 

Bunker Creek; fig. 3) over the period of record mainly reflect 

sparse underlying data in periods preceding WYs 2014–18 

(table 7).

Similar to dissolved zinc, the range and median AWQC 

ratios for dissolved cadmium have decreased at most sites 

in the study area over the period of record based on visual 

comparison of boxplots (fig. 4; table 7). The WYs 2014–18 

concentrations were still well above site-specific criteria at 

most sites, with median ratios ranging from 1.2 (Pine Creek) 

to 94 (Government Gulch; table 7). Several sites have always 

or usually been below site-specific criteria (SFCDR near 

Mullan, NFCDR at Enaville, St. Joe River at Ramsdell, and 

Spokane River below lake outlet) during the period of record 

except during occasional high streamflow events (fig. 4). 

The apparent increase in dissolved cadmium AWQC over the 

period of record at Bunker Creek (fig. 4) reflects the sparse 

underlying data (only two samples) in the periods preceding 

WYs 2014–18 (table 7).

The range and median AWQC ratios for dissolved lead 

have generally either remained about the same or decreased 

at most sites in the study area over the period of record based 

on simple visual comparison of boxplots (fig. 5). The AWQC 

ratios indicate that dissolved lead concentrations met sitespecific criteria most of the time for most sites in the study 

area; exceptions primarily occurred during high streamflow 

events (fig. 5). However, several sites generally did not meet 

site-specific criteria (Canyon Creek, Ninemile Creek, Milo 

Creek, CDR near Cataldo, CDR at Rose Lake and CDR near 

Harrison), with WYs 2014–18 median AWQC ratios ranging 

from 1.2 (Canyon Creek) to 11 (Milo Creek). Of these sites, 

the range and median AWQC ratios have generally decreased 

over the period of record in Canyon Creek, Ninemile Creek 

and CDR near Cataldo (fig. 5). However, the range and 

median AWQC ratios have remained about the same in CDR 

at Rose Lake and CDR near Harrison (fig. 5). The apparent 

increases in the Milo Creek and Bunker Creek AWQC ratios 

are caused by sparse data (three and two samples, respectively) in periods preceding WYs 2014–19 (table 7).

Model Performance

Annual mean concentrations and annual total loads were 

generated by the WRTDS_K models, and trends in concentrations and loads were calculated from flow-normalized annual 

mean concentrations and annual total loads generated by 

the WRTDS models and bootstrapped confidence intervals. 

It is therefore worthwhile to discuss the underlying model 

development and performance before describing the trends. 

In total, 85 models were developed, comprising 9 constituents 

and 12 sites (table 3). Dissolved zinc models were successfully developed at all 12 sites; orthophosphate models were 

only developed for 3 sites due to high proportions of censored 

data. Models were developed for all nine constituents at 

SFCDR near Pinehurst and CDR near Harrison, but for only 

three parameters at CDR near Cataldo due to a gap in data 

collection in the mid-2000s. Generally, the longest records 

were for SFCDR near Pinehurst, and the shortest were for the 

SFCDR at Kellogg, the Spokane River below lake outlet and 

the St. Joe River at Ramsdell. Based on careful review of the 

underlying data, models, and diagnostics (appendix 2), several 

implausibly high or low outliers that had undue influence on 

the models were removed from datasets. However, in most 

instances, outliers were retained regardless of their influence 

on the models because they likely represent actual environment conditions.

Model performance was evaluated in part by using the 

flux bias statistic. For the WRTDS model, the flux bias statistic 

provides an indication of how closely the model estimated 

flux values align with actual sampled flux (that is, the sampled 

concentrations multiplied by discharge). Note that this bias 

measure is designed to be specific to bias in flux (rather than 

concentration), and thus a great deal of weight in the calculation is associated with the days of high discharge. The flux 

bias statistics are reported in table 3 and displayed by parameter and site in fig. 6. Generally, the WRTDS models somewhat 

underpredicted flux for most parameters (fig. 6a). The WRTDS 

model performed best for dissolved cadmium, dissolved zinc, 

and orthophosphate; overall model bias for these constituents 

fell within -0.1 and 0.1. More than half of the model biases for 

total nitrogen and total zinc also fell within these bands. The 

WRTDS models performed least well for total lead and total 

phosphorus, although even for these constituents the flux bias 

statistic for most of the models was less than -0.5 (fig. 6a). 

Based on the known transport behavior of constituents in the 

study area (Clark and Mebane, 2014), the models performed 

best for constituents that have a strong negative correlation 

between streamflow and concentration (that is, dissolved 

cadmium and dissolved zinc) and performed less well for 

constituents that are transported at high concentrations in particulate form at very high streamflows (that is, total lead, total 

phosphorus, total zinc, and total cadmium). The varied model 

performances likely reflect limitations in the underlying dataset; there were many samples with varying dissolved zinc and 

cadmium concentrations across a range of streamflows, but 

samples with high concentrations of total constituents at high 

streamflows were relatively sparser due to the rarer nature of 

these streamflow events.
24 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

1990−1993

1994−1998

1999−2003

2004−2008

2009−20132014−2018

1990−1993

1994−1998

1999−2003

2004−2008

2009−20132014−2018

1990−1993

1994−19981999−2003

2004−2008

2009−2013

2014−20181990−19931994−1998

1999−2003

2004−2008

2009−2013

2014−2018

2.5

5.0

7.5

10.0

12.5

0

50

100

2.5

5.0

7.5

10.0

3

6

9

0.25

0.50

0.75

1.00

1.25

0

10

20

30

40

2.5

5.0

7.5

10.0

4

8

12

16

0.0

0.3

0.6

0.9

0.25

0.50

0.75

1.00

0

20

40

60

2.5

5.0

7.5

0

200

400

600

0

5

10

15

20

2

4

6

8

0.00

0.25

0.50

0.75

1.00

2.5

5.0

7.5

10.0

12.5

5

10

1.0

1.5

2.0

2.5

2.5

5.0

7.5

10.0

Ambient water quality criteria ratio for dissolved cadmium

CDR at Rose Lake CDR near Harrison St. Joe River at Ramsdell Spokane River below lake outlet

Pine Creek SFCDR near Pinehurst NFCDR at Enaville CDR near Cataldo

Bunker Creek Government Gulch SFCDR at Smelterville SFCDR above Pine Creek

SFCDR at Elizabeth Park Milo Creek SFCDR at Kellogg Seeps north of tailings

SFCDR near Mullan Canyon Creek Ninemile Creek SFCDR at Wallace 

1.5 times the upper interquartile range

75th percentile

Median

25th percentile

1.5 times the lower interquartile range

Values beyond 1.5 times the interquartile range

Ambient water quality criteria ratio of 1

EXPLANATION

Figure 4. Dissolved cadmium ambient water-quality criteria ratios for water years 1990–2018 for sites in the Spokane River 

watershed, northern Idaho. Site locations are shown in figure 1. Data were not available for all sites for all water years. Boxplots 

present as lines where the underlying data are limited to fewer than four samples. Abbreviations: CDR, Coeur d’Alene River; 

NFCDR, North Fork Coeur d’Alene River; SFCDR, South Fork Coeur d’Alene River.
Results 25

CDR at Rose Lake CDR near Harrison St. Joe River at Ramsdell Spokane River below lake outlet

Pine Creek SFCDR near Pinehurst NFCDR at Enaville CDR near Cataldo

Bunker Creek Government Gulch SFCDR at Smelterville SFCDR above Pine Creek

SFCDR at Elizabeth Park Milo Creek SFCDR at Kellogg Seeps north of tailings

SFCDR near Mullan Canyon Creek Ninemile Creek SFCDR at Wallace 

1990−19931994−1998

1999−20032004−2008

2009−2013

2014−2018

1990−1993

1994−19981999−20032004−2008

2009−2013

2014−2018

1990−1993

1994−1998

1999−2003

2004−2008

2009−2013

2014−2018

1990−1993

1994−1998

1999−2003

2004−2008

2009−2013

2014−2018

0.3

0.5

1.0

0.001

0.010

0.100

1.000

0.1

0.3

1.0

0.3

1.0

3.0

10.0

30.0

0.1

1.0

10.0

1

3

5

0.1

0.3

1.0

0.03

0.10

0.30

1.00

0.1

0.3

1.0

0.1

0.3

1.0

0.5

1.0

3.0

5.0

1

3

10

0.3

0.5

1.0

0.1

1.0

10.0

1

10

100

0.01

0.10

1.00

0.1

0.3

1.0

0.01

0.10

1.00

0.03

0.10

0.30

1.00

1

3

10

30

Ambient water quality criteria ratio for dissolved lead

1.5 times the upper interquartile range

75th percentile

Median

25th percentile

1.5 times the lower interquartile range

Values beyond 1.5 times the interquartile range

Ambient water quality criteria ratio of 1

EXPLANATION

Figure 5. Dissolved lead ambient water-quality criteria (AWQC) ratios for water years 1990–2018 for sites in the Spokane River 

watershed, northern Idaho. Site locations are shown in figure 1. Data were not available for all sites for all water years. Boxplots 

present as lines where the underlying data are limited to fewer than four samples. Abbreviations: CDR, Coeur d’Alene River; 

NFCDR, North Fork Coeur d’Alene River; SFCDR, South Fork Coeur d’Alene River.
26 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

−1.5

−1.0

−0.5

0.0

Site (drainage area, in square miles)

Flux bias statistic

Flux bias statistic for each constituent at each site

Range of flux bias statistic for all constituents 

at each site

Cadmium, dissolved

Cadmium, total

Lead, dissolved

Lead, total

Nitrogen, total

Orthophosphate

Phosphorus, total

Zinc, dissolved

Zinc, total

−1.5

−1.0

−0.5

0.0

Cadmium, dissolved

Cadmium, total

Lead, dissolved

Lead, total

Nitrogen, total

Orthophosphate

Phosphorus, total

Zinc, dissolved

Zinc, total

Constituent

Flux bias statistic

EXPLANATION

EXPLANATION

1.5 times the upper interquartile range

75th percentile

Median

25th percentile

1.5 times the lower interquartile range

Values beyond 1.5 times the interquartile range

Flux bias statistic at 0.10 and −0.10

Range of flux bias statistic for each constituent

1.5 times the upper interquartile range

75th percentile

Median

25th percentile

1.5 times the lower interquartile range

Values beyond 1.5 times the interquartile range

Flux bias statistic at 0.10 and −0.10

A

B

Ninemile Creek (11.6)

Canyon Creek (22)

Pine Creek (73.2)

SFCDR at Elizabeth Park (182)

SFCDR at Kellogg (194)

SFCDR at Smelterville (202)

SFCDR near Pinehurst (287)

NFCDR at Enaville (895)

CDR near Cataldo (1,208)

CDR near Harrison (1,453)

St. Joe River at Ramsdell (1,721)

Spokane River below lake outlet (3,700)

Figure 6. Flux bias statistics associated with Weighted Regressions on Time, Discharge and Season (WRTDS) models for water 

years 1990-2018, grouped by (A) parameter and (B) site, Spokane River watershed, northern Idaho. Site locations are shown in 

figure 1. Models were not generated for all constituents at all sites. Abbreviations: CDR, Coeur d’Alene River; NFCDR, North Fork 

Coeur d’Alene River; SFCDR, South Fork Coeur d’Alene River.
Results 27

Looking at model performance by site (fig. 6b; table 3), 

the flux bias statistics were closest to 0 for sites with the most 

data or the longest records (NFCDR at Enaville, SFCDR 

at Elizabeth Park, SFCDR near Pinehurst, and CDR near 

Harrison). Sites with shorter records (SFCDR at Kellogg and 

SFCDR at Smelterville), smaller streams (Canyon Creek and 

Ninemile Creek) and sites with sparse data over intervals in 

the middle of the record (CDR near Cataldo) generally had 

bigger (that is, further from 0) flux bias statistics (fig. 6b; 

table 3). Poor model performance tended to happen at sites 

with smaller drainage areas. It is generally more difficult to 

obtain enough samples at the highest discharges at these sites 

because the duration of very high discharge tends to be short. 

The information on flux bias can be useful in planning for 

future sampling efforts; for example, sites where the flux bias 

statistic is large in absolute value are good candidates for high 

emphasis on high flow sampling in the future. Moreover, for 

most sites the biggest flux bias statistics were associated with 

models for constituents with particulate transport (for example, total lead and total phosphorus). This was particularly 

true for sites higher in the CDR watershed (tributaries and 

the SFCDR sites upstream of Pinehurst) which have smaller 

numbers of high streamflow (and hence, high concentration) 

samples. This is partly a function of shorter records at many of 

these sites and partly of the flashy nature of high-streamflow, 

high-transport events. The flux bias statistics for dissolved 

lead were higher at the downstream end of the CDR watershed 

(SFCDR near Pinehurst, CDR near Cataldo, and CDR near 

Harrison) and may reflect more complicated transport dynamics for this constituent at the downstream end of the CDR 

watershed (fig. 6b). Generally, higher dissolved lead concentrations are associated with higher streamflows, but dissolved 

lead concentrations can also increase at low streamflows, 

particularly at the CDR sites (Zinsser, 2018).

At present (2020), there is no a method to systematically 

evaluate bias in the WRTDS_K models. However, because the 

Kalman filtering procedure in WRTDS_K uses actual sample 

concentrations in place of model estimates on days with 

samples and weights estimates on proximal days accordingly, 

the WRTDS_K models may do a better job than WRTDS at 

estimating high particulate transport events. The WRTDS_K 

models, however, would fundamentally still be limited by how 

well the underlying samples represent transport dynamics during high streamflow events. For example, in a system where 

hysteresis is important, improved estimates are feasible if the 

underlying samples generally included samples from both the 

rising and falling limbs of major flow events. Nonetheless, 

given the high negative biases associated with particulate 

constituents in this report, WRTDS_K estimates may provide 

a substantial improvement over WRTDS estimates, but there is 

not currently a systematic way to describe this effect for these 

data. The basis for choosing to use the WRTDS_K stems from 

Lee and others (2019), where these estimates were compared 

with other common methods and found to be more accurate.

In summary, review of the flux bias statistics (and other 

model diagnostics, appendix 2) suggest that flow-normalized 

annual mean concentration and annual total load results 

somewhat underpredict actual values overall, and these 

underestimates are likely to be greatest for constituents with 

high-streamflow, particulate-driven transport (that is, total lead 

and total phosphorus). Based on statistical theory and previous 

experiments, it is likely the case that WRTDS_K estimates for 

annual mean concentration and annual total load results have 

less negative bias (Lee and others, 2019; Zhang and Hirsch, 

2019) than WRTDS estimates, but this effect cannot currently 

be quantified for these models. Thus, as with all models, 

interpretation of concentrations, loads, and trends are susceptible to weaknesses in the underlying models. Nonetheless, 

the WRTDS_K estimates presented here are based on robust 

statistical techniques and likely represent more accurate 

estimates than previous LOADEST-derived estimates or the 

original WRTDS estimates based on extensive model comparison work completed by Lee and others (2019) and Zhang and 

Hirsch (2019).

Trends in Concentrations and Loads

At the most basic level, WRTDS_K annual mean 

concentrations and loads can be used to give a general sense 

of average conditions at sites in the study area. To this end, 

the annual mean concentration and load for each parameter 

at each modeled site are shown in figure 7, and the WYs 

2014–18 5-year mean of the annual mean concentrations are 

presented in table 8. This table and figure provide a general 

overview of constituent concentrations and loads in the study 

area over the most recent 5-year period. For example, figure 7

shows that concentrations generally decreased from upstream 

to downstream in the study area and loads generally increased. 

Concentrations and loads in the NFCDR (which is much less 

affected by mining than the SFCDR) and in the St. Joe River 

(which is unaffected by mining) were low relative to SFCDR, 

CDR main stem, and Spokane River sites. Concentrations 

in mining-affected tributaries (Ninemile, Canyon, and Pine 

Creeks) tended to be high, but loads from these tributaries were relatively low due to low streamflows. In contrast, 

concentrations in CDR near Harrison were low (cadmium 

and zinc) or comparable (lead) to the SFCDR sites, but loads 

were high due to more streamflow (fig. 7). In the SFCDR and 

tributary sites, most of the cadmium and zinc (greater than 90 

percent) was present in the dissolved fraction, whereas most of 

the lead (greater than 65 percent) was present in the particulate fraction. While those same overall patterns were true for 

CDR near Harrison, the particulate fractions for zinc (about 

15 percent), cadmium (about 25 percent), and lead (about 90 

percent) were all somewhat higher than in the SFCDR sites 

(table 8). Note that particulate concentrations were not directly 

measured in these data but instead are inferred as the difference between the total constituent concentration and the dissolved (filtered) constituent concentrations. For the three sites 
28 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

Zinc, concentration Zinc, load

Lead, concentration Lead, load

Cadmium, concentration Cadmium, load Canyon Creek Ninemile Creek SFCDR at Elizabeth Park SFCDR at Kellogg SFCDR at Smelterville Pine Creek SFCDR near Pinehurst NFCDR at Enaville CDR near Cataldo CDR near Harrison St. Joe River at Ramsdell Spokane River below lake outlet Canyon Creek Ninemile Creek SFCDR at Elizabeth Park SFCDR at Kellogg

SFCDR at Smelterville

Pine Creek

SFCDR near Pinehurst

NFCDR at Enaville

CDR near Cataldo

CDR near Harrison

St. Joe River at Ramsdell

Spokane River below lake outlet

0.1

1.0

10.0

0.1

1.0

10.0

100

1,000

10

100

1,000

0.1

1.0

10.0

0.1

1.0

10.0

100

1

10

100

1,000

Site Site

Concentration, in micrograms per year

Dissolved

Total

EXPLANATION

1.5 times the upper 

interquartile range

75th percentile

Median

25th percentile

1.5 times the lower 

interquartile range

Values beyond 1.5 times the 

interquartile range

Figure 7. Annual mean concentrations and loads for cadmium, lead, and zinc from Weighted Regressions on Time, Discharge and 

Season with Kalman filtering (WRTDS_K) models for water years 2014–18 for sites in the Spokane River watershed, northern Idaho. 

Site locations are shown in figure 1. Data were not available for all sites for all water years. Abbreviations: CDR, Coeur d’Alene 

River; NFCDR, North Fork Coeur d’Alene River; SFCDR, South Fork Coeur d’Alene River.
Results 29

where both total phosphorus and orthophosphate models were 

available (SFCDR near Pinehurst, CDR near Harrison, and St. 

Joe River at Ramsdell), dissolved orthophosphate comprised 

20–40 percent of the total phosphorus (table 8).

The WRTDS_K annual mean concentration and annual 

total load and WRTDS flow-normalized annual mean concentration and annual total load for each site, parameter, and 

water year that were modeled are presented in Zinsser (2020). 

For each site, parameter, and water year that were modeled in 

WRTDS and had successful bootstrapped confidence intervals constructions (in 3 out of 170 cases, multiple bootstrap 

replicate models did not converge and confidence intervals 

could not be constructed), the total change in flow-normalized 

concentrations and loads over the period of record and during 

WYs 2009–18, as well as the statistical likelihood associated with the direction of these changes, are presented in 

Zinsser (2020). 

It may help the reader to better understand the meaning 

of the results shown in Zinsser (2020) to take two specific 

analyses and provide a short narrative of their meaning. First, 

consider the total lead load results at SFCDR at Elizabeth Park 

for the full period of record. The Zinsser (2020) entry says that 

the total load change was -21 metric tons, which means that, 

over the full period of record (WYs 1993–2018), the estimated 

change in annual load was a decrease of 21 metric tons. To 

produce this estimate, all the data during this period were 

evaluated and used to construct a smooth representation of 

change, and the value at the end of this representation was 21 

metric tons lower than the value at the beginning (that is, the 

change is not just a comparison of the first and last years). This 

change was equivalent to a 48 percent decrease in total load 

(change divided by the initial year value). The statistical likelihood of the change was 0.12 and called “likely down.” What 

this means is that, although we cannot state with certainty that 

there was a decrease over this period, there was only about 

a 0.12 probability that the trend was actually upwards and, 

consequently, a 0.88 probability that the trend was actually 

downward. In short, the evidence for downtrend is strong, but 

not ironclad. In contrast to that result, we can look at the total 

lead load trend at SFCDR at Elizabeth Park for WYs 2009–18. 

The estimated change in annual load over the period was 

-1.6 metric tons. This change was equivalent to a 6.6 percent 

decrease over the period, which suggests that the change in 

this time period was much smaller than over the full of record. 

However, the trend likelihood was 0.44 which causes this 

result to be categorized as “about as likely as not.” What that 

means is that even though the best estimate of the change was 

downwards, there was actually a 0.44 probability that the true 

change was upwards, and thus the probability that the change 

was downwards was 0.56. Because this is rather close to a 

50/50 result, we state that it falls in the class of trends that are 

about as likely to be upwards as they are to be downwards. 

The idea of approaching trend results from this vantage point 

has been promoted in recent years by Hirsch and others (2015)

and McBride (2019). It is a departure from traditional null 

hypothesis significance testing and rather focuses on quantifying for the reader the degree to which the analyst is certain or 

uncertain about the true direction of the trend.

Table 8. Five-year mean of annual mean concentrations for total and dissolved constituents derived from Weighted Regression 

on Time, Discharge and Season with Kalman filtering models for sites in the Spokane River watershed, northern Idaho, water years 

2014–18.

[Sufficient data were not available at all sites for all water years, and models were not generated for all constituents at all sites. Abbreviations: CDR, Coeur 

d'Alene River; NA, not applicable; NFCDR, North Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River; WRTDS_K, Weighted Regressions on 

Time, Discharge and Season with Kalman filtering; μg/L, microgram per liter]

Site name 

(short, as used 

in this report)

Dissolved 

cadmium 

(μg/L)

Total 

cadmium 

(μg/L)

Dissolved 

lead 

(μg/L)

Total 

lead 

(μg/L)

Dissolved 

zinc 

(μg/L)

Total 

zinc 

(μg/L)

Orthophosphate 

(μg/L)

Total 

phosphorus 

(μg/L)

NFCDR at Enaville 0.018 0.019 0.098 0.514 3.51 4.06 NA 7.71

Canyon Creek 9.31 9.35 9.37 38.0 1560 1536 NA 5.48

Ninemile Creek 13.4 13.3 15.5 51.4 2244 2170 NA NA

SFCDR at Elizabeth Park 3.50 3.69 1.85 24.8 537 565 NA 10.3

SFCDR at Kellogg 3.49 3.64 2.81 24.7 543 541 NA 9.71

SFCDR at Smelterville 5.85 5.96 2.26 25.7 777 816 NA 33.8

Pine Creek NA 0.25 NA 0.763 77.9 75.8 NA NA

SFCDR near Pinehurst 4.13 4.32 1.97 20.1 660 665 15.5 39.9

CDR near Cataldo 1.18 NA 0.84 NA 198 NA NA NA

CDR near Harrison 0.88 1.24 6.25 68.0 167 211 3.46 17.3

St. Joe River at Ramsdell NA NA 0.114 0.225 1.68 2.28 5.84 22.4

Spokane River below lake outlet 0.14 0.16 0.401 1.11 36.7 38.2 NA 5.81
30 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

Zinc

The WRTDS and WRTDS_K model results indicate 

dramatic declines in dissolved zinc over the period of record. 

Figure 8 shows the WRTDS_K annual mean concentrations 

and annual total loads and the WRTDS flow-normalized 

annual mean concentrations and annual total loads for select 

sites (SFCDR near Pinehurst, CDR near Harrison, and 

Spokane River below lake outlet; complete results are in 

appendix 1). For each of these sites, decreases in dissolved 

zinc concentrations and loads were observed for the period of 

record, although the magnitude of the changes and the length 

of the period of record varies between sites. At SFCDR near 

Pinehurst and CDR near Harrison, the slope of the change was 

steepest during the 1990s and less steep thereafter (fig. 8).

In the entire study area over the period of record, flownormalized dissolved zinc concentrations and loads have 

decreased dramatically, with a high statistical likelihood 

(“likely down” trends), at every site except the miningunaffected St. Joe River at Ramsdell (Zinsser, 2020; fig. 9). In 

the SFCDR and CDR, dissolved zinc concentration decreases 

ranged from 27 percent (-830 μg/L) at Ninemile Creek to 

63 percent in both the SFCDR near Pinehurst (-1,100 μg/L) 

and CDR near Cataldo (-310 μg/L). The dissolved zinc load 

decreases ranged from 30 percent (-53 metric tons) in SFCDR 

at Kellogg to 64 percent (-359 metric tons) in SFCDR near 

Pinehurst (Zinsser, 2020).

In WYs 2009–18, absolute decreases in dissolved 

zinc concentrations and loads were more modest relative 

to decreases over the period of record. Nonetheless, flownormalized dissolved zinc concentrations and loads have also 

decreased, with high statistical likelihood (“likely down” 

trends), in WYs 2009–18 at every site in the study area 

(Zinsser, 2020; fig. 9). In the SFCDR and CDR, dissolved 

zinc concentration decreases ranged from 8.6 percent (-210 

μg/L) at Ninemile Creek to 27 percent (-67 μg/L) in CDR near 

Cataldo. The dissolved zinc load decreases ranged from 17 

percent (-65 metric tons) in CDR near Harrison to 26 percent 

in both Pine Creek (-2.9 metric tons) and CDR near Cataldo 

(-82 metric tons; Zinsser, 2020).

The difference in load trends from earlier in the period 

of record to the most recent decade (fig. 8) was also explored 

with trend slope confidence intervals (fig. 10). For this analysis, data were limited to WYs 1999–2009 and WYs 2009–18 

for better comparability; therefore, sites with shorter periods 

of records were eliminated from this particular analysis, and 

sites with longer periods of records were truncated. The trend 

slopes were generally similar in magnitude between the two 

periods (fig. 10). This suggests that the overall rate of change 

was similar, although as concentrations and loads decreased in 

the watershed, the absolute size of the decreases also inherently got smaller. However, note that the time period with the 

steepest slopes (1990s; fig. 8) was not compared as a necessary trade-off of standardizing the time periods for analysis.

There are several puzzling trends in the dissolved zinc 

data that warrant more discussion, namely, “likely down” 

trends at NFCDR at Enaville over the period of record and 

WYs 2009–18 and at St. Joe River at Ramsdell in WYs 

2009–18. Although the absolute change in load and concentrations at these sites was relatively small, a small change to a 

small concentration or load can nonetheless represent a large 

percentage change (Zinsser, 2020; fig. 9). This is somewhat 

misleading because it causes these changes to appear comparable to those at mining-affected sites. The St. Joe River at 

Ramsdell has been unaffected by mining, and it is not clear 

that there is another source of human-caused zinc in this 

watershed. There was some limited mining in the NFCDR 

watershed, but cleanup in these areas is not under EPA jurisdiction, and it was beyond the scope of this report to explore 

the extent and impact of such potential cleanups. In the St. Joe 

River at Ramsdell, the WYs 2014–18 annual mean concentration (1.68 μg/L; table 8) was close to the current quantitation 

limit (2 μg/L). This proximity suggests that there is probably 

more uncertainty in this trend than the statistical likelihood 

implies, with the uncertainty arising not from the model but 

from the underlying data themselves. Analytical precision 

degrades when sample concentrations are close to detection 

limits (Paul and others, 2016). Annual mean concentrations in 

the NFCDR (3.51 μg/L; table 8) were higher than the detection limits, but the data collection period at this site was long 

enough to encompass periods with much higher detection 

limits (20 μg/L in the 1990s; table 5). It is well-established 

that improper treatment of censored values can affect data 

analysis (Helsel, 2006), but in the context of WRTDS, which 

relies on robust maximum likelihood estimation to incorporate censored data, it is unclear what impact large changes in 

detection limits over time may have on trends in concentration between multiple detection limits. It is also possible that 

changes in laboratory methods over time may have impacted 

these low concentration data. However, a full exploration of 

the potential impacts of these issues (which also extends to 

low-concentration trends in cadmium and lead) was beyond 

the scope of this report. In summary, it is unclear that trends in 

these rivers result from actual environmental change, but the 

possibility cannot but ruled out and thus the trends are retained 

here. However, readers are cautioned that there is a possibility 

these very low concentration trends are artifacts of changes in 

laboratory precision, methods, detection levels or some other 

issue arising from the length of the dataset.

The trends and likelihoods for flow-normalized total 

zinc concentrations and loads are reported in Zinsser (2020). 

Overall, they closely tracked the trends and likelihoods 

reported for dissolved zinc, which is consistent with established patterns of zinc transport in the study area where dissolved zinc makes up the majority of total zinc except during 

very high streamflows (table 8; Clark and Mebane [2014]). 

One notable difference between dissolved and total zinc load 

trends was that the statistical likelihood of a downward trend 

in total zinc load at CDR near Harrison for WYs 2009–18 

was only “somewhat likely down.” This difference likely 

reflects the relatively greater transport of particulate zinc in the 

lower CDR and the fact that different processes govern this 

transport.
Results 31

Cadmium

The WRTDS and WRTDS_K model results indicate 

dramatic decreases in dissolved cadmium over the period of 

record. Figure 11 shows the WRTDS_K annual mean concentrations and annual total loads and the WRTDS flownormalized annual mean concentrations and annual total loads 

for select sites (SFCDR near Pinehurst, CDR near Harrison 

and Spokane; complete results are in appendix 1). At each 

of these sites, decreases in dissolved zinc concentrations and 

loads occurred, although the period of record and magnitude 

of the changes varied between sites. The slope of the change 

was steepest in the 1990s and least steep in the most recent 

decade (fig. 11).

In the entire study area over the period of record, flownormalized dissolved cadmium concentrations and loads 

decreased with a high degree of statistical likelihood (“likely 

down” trends) over the period of record at all the modeled 

1990 1995 2000 2005 2010 2015

600

900

1,200

1,500

1,800

150

200

250

300

350

35

40

45

50

Dissolved zinc concentration, in micrograms per liter

South Fork Coeur d’Alene River near Pinehurst

1990 1995 2000 2005 2010 2015

200

300

400

500

600

200

400

600

800

200

300

400

Dissolved zinc load, in metric tons per year

Water year Water year

Spokane River below lake outlet

Coeur d’Alene River near Harrison

South Fork Coeur d’Alene River near Pinehurst

Spokane River below lake outlet

Coeur d’Alene River near Harrison

WRTDS_K annual mean concentration 

WRTDS flow-normalized annual mean concentration

WRTDS_K annual total load

WRTDS flow-normalized annual total load

EXPLANATION EXPLANATION

Figure 8. Dissolved zinc annual mean concentrations and annual total loads from Weighted Regressions on Time, Discharge and 

Season with Kalman filtering (WRTDS_K) and flow-normalized annual mean concentrations and annual total loads from Weighted 

Regressions on Time, Discharge and Season (WRTDS) for select sites in the Spokane River watershed, northern Idaho, water years 

1990–2018. Sites are shown in figure 1. Abbreviations: WRTDS, Weighted Regressions on Time, Discharge and Season; WRTDS_K, 

Weighted Regressions on Time, Discharge and Season with Kalman filtering.
32 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

sites (Zinsser, 2020; fig. 12). The percent decrease in concentrations varied from 26 percent (-0.049 μg/L) in the Spokane 

River below lake outlet to 67 percent (-2.1 μg/L) in the CDR 

near Cataldo. The percent load reductions varied from 25 

percent (-0.31 metric tons) in the Spokane River below lake 

outlet to 70 percent (-3.3 metric tons) in the CDR near Cataldo 

(Zinsser, 2020).

From WY 2009 to 2018, flow-normalized dissolved cadmium concentrations and loads decreased with a high degree 

of statistical likelihood (“likely down” trends) at all modeled 

sites, albeit with more modest declines than over the period 

of record (Zinsser, 2020; fig. 12). The decreases in concentrations ranged from 12 percent (-1.8 μg/L) in Ninemile Creek to 

29 percent (-0.44 μg/L) in CDR near Cataldo. The decreases 

in load ranged from 12 percent (-0.25 metric tons) in CDR 

near Harrison to 28 percent (-0.55 metric tons) in CDR near 

Cataldo (Zinsser, 2020).

The difference in load trends from earlier in the period 

of record to the most recent decade (fig. 11) was explored 

with trend slope confidence intervals (fig. 10). For most of 

the sites used in this analysis, the trend slopes were somewhat less steep during WYs 2009–18 than during WYs 

1999–2009 (fig. 10). This decrease in trend slope suggests 

that remedial actions had a relatively greater impact reducing 

dissolved cadmium loads from WY 1999 to 2009 than during 

WYs 2009–18.

The trends and likelihoods for flow-normalized total 

cadmium concentrations and loads are markedly similar to 

the trends and likelihoods for dissolved cadmium (Zinsser, 

Likelihood descriptor—Shown by 

symbol shape and color

Likely up

Somewhat likely up

About as likely as not

Somewhat likely down

Likely down

No model

Magnitude of change, in percentage—

Shown by symbol size

0 to 25

26 to 50

51 to 80

EXPLANATION

[This explanation shows all possible symbols in order to maintain consistency between this figure 

and similar figures in this report, but not all symbols appear in each figure. The absence of a symbol 

in any individual figure is intentional and means that it does not apply to that individual figure.]

River—Arrow shows direction of flow

PinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth ParkPinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth Park

PinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth ParkPinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth Park

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

A. Dissolved zinc concentration, period of record

C. Dissolved zinc concentration, 2009–18 D. Dissolved zinc load, 2009–18

B. Dissolved zinc load, period of record

Figure 9. Statistical likelihood and magnitude of change in flow-normalized dissolved zinc concentrations and annual total loads over 

the period of record and water years 2009–18 for sites in the Spokane River watershed, northern Idaho. Sites are shown in figure 1. 

Statistical likelihoods are defined in table 4. Period of record is defined for each site and constituent in table 3. Diagram is not to scale.
Results 33

2020). This reflects the dominance of the dissolved fraction in 

total cadmium. One difference in the results, however, was the 

failure of multiple total cadmium bootstrap replicate models 

to converge, which led to null results for total cadmium load 

likelihoods in Pine Creek for the period of record (Zinsser, 

2020). For Pine Creek, this lack of model convergence likely 

arose from a data collection gap between WYs 2004 and 2007 

and the relative smallness of the dataset (n = 69, with 9 censored values; table 3).

Lead

The WRTDS and WRTDS_K model results indicate variable trends in total lead over the period of record. Figure 13

shows the WRTDS_K annual mean concentrations and annual 

total loads and the WRTDS flow-normalized annual mean 

concentrations and annual total loads for select sites (SFCDR 

near Pinehurst, CDR near Harrison, and Spokane River below 

lake outlet; complete results are in appendix 1). Decreases in 

total lead concentrations and loads occurred at both SFCDR 

and Pinehurst and Spokane River below lake outlet over the 

period of record (which varies from 1990 to 2018 at SFCDR 

near Pinehurst to 2003-2018 at Spokane River below lake outlet), although the magnitude of the change was much greater 

at SFCDR near Pinehurst. Total lead concentrations and loads 

in CDR near Harrison had variable trends, with both increases 

and decreases over the period of record (fig. 13).

In the entire study area over the period of record, flownormalized concentrations of total lead decreased with a 

high degree of statistical likelihood (“likely down” trends) at 

Total lead Total phosphorus

Dissolved zinc Dissolved cadmium Canyon Creek Ninemile Creek SFCDR at Elizabeth Park SFCDR at Smelterville Pine Creek SFCDR near Pinehurst NFCDR at Enaville CDR near Cataldo CDR near Harrison Canyon Creek Ninemile Creek SFCDR at Elizabeth Park

SFCDR at Smelterville

Pine Creek

SFCDR near Pinehurst

NFCDR at Enaville

CDR near Cataldo

CDR near Harrison

−4

−2

0

−4

0

4

−4

−2

0

2

−10

−5

0

5

10

Site Site

Slope of load trend, in percent per year

Time period—Symbol 

shows median; vertical 

bars show 90 percent 

confidence interval

1999−2009

2002−09

2009−18

EXPLANATION

Figure 10. Change in load per year (slope of load trends) and 90 percent confidence intervals for select constituents and sites in the 

Spokane River watershed, northern Idaho, water years 1999–2018. Sites are shown in figure 1. Abbreviations: CDR, Coeur d'Alene River; 

NFCDR, North Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River.
34 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

most sites (Zinsser, 2020; fig. 14). The trend was “somewhat 

likely down” for SFCDR at Kellogg, and a downward trend 

was “about as likely as not” for the St. Joe River at Ramsdell 

(where concentrations are very low relative to the rest of 

study area). For sites with “likely down” trends, the decreases 

ranged from 25 percent (-22 μg/L) for CDR near Harrison 

to 76 percent (-59 μg/L) for SFCDR near Pinehurst (Zinsser, 

2020). The trends were more variable for flow-normalized 

total lead loads. Most SFCDR sites and tributaries and the 

Spokane River below lake outlet had “likely down” trends, 

with the percent change ranging from 32 percent (-4.5 metric 

tons) in the Spokane River below lake outlet to 78 percent 

(-86 metric tons) in the SFCDR near Pinehurst. A downward 

trend was “about as likely as not” for SFCDR at Kellogg, and 

the trend was “somewhat likely down” for the St. Joe River at 

Ramsdell. Notably, the total lead load trend was “somewhat 

likely up” in the CDR near Harrison, with a positive change of 

24 percent (168 metric tons; Zinsser, 2020).

4

6

8

10

1.00

1.25

1.50

1.75

0.14

0.15

0.16

0.17

Dissolved cadmium concentration, in micrograms per liter

0.18

2

3

4

1

2

3

4

5

0.9

1.2

1.5

Dissolved cadmium load, in metric tons per year

WRTDS_K annual mean concentration 

WRTDS flow-normalized annual mean concentration

WRTDS_K annual total load

WRTDS flow-normalized annual total load

EXPLANATION EXPLANATION

1990 1995 2000 2005 2010 2015 1990 1995 2000 2005 2010 2015

Water year Water year

South Fork Coeur d’Alene River near Pinehurst

Spokane River below lake outlet

Coeur d’Alene River near Harrison

South Fork Coeur d’Alene River near Pinehurst

Spokane River below lake outlet

Coeur d’Alene River near Harrison

Figure 11. Dissolved cadmium annual mean concentrations and annual total loads from Weighted Regressions on Time, Discharge 

and Season with Kalman filtering and flow-normalized annual mean concentrations and annual total loads from Weighted Regressions 

on Time, Discharge and Season for select sites in the Spokane River watershed, northern Idaho, water years 1990-2018. Sites are 

shown in figure 1. Abbreviations: WRTDS, Weighted Regressions on Time, Discharge and Season; WRTDS_K, Weighted Regressions 

on Time, Discharge and Season with Kalman filtering.
Results 35

From WY 2009 to 2018, most SFCDR sites, the tributary 

sites, and the Spokane River below lake outlet had “likely 

down” trends in flow-normalized total lead concentrations 

(Zinsser, 2020; fig. 14). For sites with “likely down” trends, 

the concentration decreases ranged from 24 percent (14 μg/L) 

in Ninemile Creek to 47 percent (-0.55 μg/L) in Pine Creek. 

Flow-normalized total lead concentration trends were “somewhat likely down” in the NFCDR at Enaville, SFCDR at 

Kellogg, CDR near Harrison, and St. Joe River at Ramsdell. 

The decreases at these sites were generally smaller than those 

for the “likely down” trends, ranging from 14 percent (-0.092 

μg/L) in the NFCDR at Enaville to 24 percent (-6.9 μg/L) 

in the SFCDR at Kellogg. For one site, SFCDR at Elizabeth 

Park, a downward trend was “about as likely as not”. The 

flow-normalized total lead load trends from WY 2009 to 2018 

were similarly variable. Several sites had “likely down” trends 

(NFCDR at Enaville, Ninemile Creek, SFCDR near Pinehurst, 

St. Joe River at Ramsdell and Spokane River below lake outlet). The decreases at these sites ranged from 22 percent (-0.46 

metric tons) at Ninemile Creek to 33 percent (-12 metric tons) 

in SFCDR near Pinehurst. Two sites had “somewhat likely 

down” trends (Canyon Creek and SFCDR at Smelterville), and 

a downward trend was “about as likely as not” at three sites 

(SFCDR at Elizabeth Park, SFCDR at Kellogg and CDR near 

Harrison; Zinsser, 2020).

The slope confidence intervals for total lead help to illustrate differences between load trends for earlier and later time 

periods (fig. 10). For most of the sites used in this analysis, the 

Likelihood descriptor—Shown by 

symbol shape and color

Likely up

Somewhat likely up

About as likely as not

Somewhat likely down

Likely down

No model

Magnitude of change, in percentage—

Shown by symbol size

0 to 25

26 to 50

51 to 80

EXPLANATION

[This explanation shows all possible symbols in order to maintain consistency between this figure 

and similar figures in this report, but not all symbols appear in each figure. The absence of a symbol 

in any individual figure is intentional and means that it does not apply to that individual figure.]

River—Arrow shows direction of flow

PinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth ParkPinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth Park

PinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth ParkPinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth Park

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

A. Dissolved cadmium concentration, period of record

C. Dissolved cadmium concentration, 2009–18 D. Dissolved cadmium load, 2009–18

B. Dissolved cadmium load, period of record

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Figure 12. Statistical likelihood and magnitude of change in flow-normalized dissolved cadmium concentrations and loads over 

the period of record and water years 2009–18 for sites in the Spokane River watershed, northern Idaho. Sites are shown in figure 1. 

Statistical likelihoods are defined in table 4. Period of record is defined for each site and constituent in Table 3. Diagram is not to scale. 

Abbreviations: CDR, Coeur d'Alene River; NFCDR, North Fork Coeur d'Alene River; SFCDR, South Fork Coeur d'Alene River.
36 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

trend slopes were somewhat less steep during WYs 2009–18 

than during WYs 1999–2009. This suggests that remedial 

actions had a relatively greater impact reducing total lead 

loads from WY 1999 to 2009 than during WYs 2009–2018. 

The CDR near Harrison shows a markedly different trend 

though, with lead loads increasing from WY 1999 to 2009 and 

then decreasing (but near 0) from WYs 2009–2018 (fig. 10).

Generally, trends and likelihoods in flow-normalized dissolved lead concentrations and loads were similar to the trends 

for total lead (Zinsser, 2020). Most sites had “likely down” 

or “somewhat likely down” trends during WYs 2009–2018 

and the period of record. There were a couple of exceptions. 

Dissolved lead concentrations and loads had “likely up” trends 

at St. Joe River at Ramsdell over both the period of record 

and WYs 2009–18. The changes in concentrations and loads 

30

60

90

50

100

150

1.0

1.5

2.0

Total lead concentration, in micrograms per liter

0

50

100

150

200

0

1,000

2,000

3,000

4,000

5,000

10

20

30

40

Total lead load, in metric tons per year

WRTDS_K annual mean concentration 

WRTDS flow-normalized annual mean concentration

WRTDS_K annual total load

WRTDS flow-normalized annual total load

EXPLANATION EXPLANATION

1990 1995 2000 2005 2010 2015 1990 1995 2000 2005 2010 2015

Water year Water year

South Fork Coeur d’Alene River near Pinehurst

Spokane River below lake outlet

Coeur d’Alene River near Harrison

South Fork Coeur d’Alene River near Pinehurst

Spokane River below lake outlet

Coeur d’Alene River near Harrison

Figure 13. Total lead annual mean concentrations and annual total loads from Weighted Regressions on Time, Discharge and Season 

with Kalman filtering (WRTDS_K) and flow-normalized annual mean concentrations and annual total loads from Weighted Regressions 

on Time, Discharge and Season (WRTDS) for select sites in the Spokane River watershed, northern Idaho, water years 1990–2018. 

Sites are shown in figure 1. Abbreviations: WRTDS, Weighted Regressions on Time, Discharge and Season; WRTDS_K, Weighted 

Regressions on Time, Discharge and Season with Kalman filtering.
Results 37

were small in absolute terms as concentrations at this site 

were still quite low (0.114 μg/L; table 8), overlapped with 

lead contamination in blanks (median 0.074 μg/L to maximum 4.82 μg/L; table 5), and were well below the dissolved 

lead AWQC (table 7). Nonetheless, the load change was 42 

percent (0.1 metric tons) during WYs 2009–18 and 66 percent 

(0.14 metric tons) over the period of record. Dissolved lead 

loads in the NFCDR at Enaville also have increasing trends 

over the period of record (40 percent, “likely up”) and WYs 

2009–18 (23 percent, “somewhat likely up”). Similar to the 

St. Joe River at Ramsdell, although these trends were large 

on a relative basis, the actual dissolved lead concentrations 

are still quite low and exceed AWQC only rarely during high 

streamflow events. Finally, there are small, “somewhat likely 

up” trends in dissolved lead concentrations and loads in 

Spokane River below lake outlet over the period of record, but 

trends in WYs 2009–18 were “about as likely as not” (Zinsser, 

2020). As discussed in the “Quality Control Samples” section, 

there was some evidence of filter contamination for dissolved 

lead in low-concentration samples that may be affecting 

these trends, but data were retained in these analyses to be as 

conservative as possible in reporting potentially real environmental trends. One line of evidence for these trends reflecting 

actual environmental change was that bigger increases were 

observed over the period of record than in WYs 2009–18, but 

filter contamination issues were only identified in WYs 2011 

and WYs 2017–18.

Likelihood descriptor—Shown by 

symbol shape and color

Likely up

Somewhat likely up

About as likely as not

Somewhat likely down

Likely down

No model

Magnitude of change, in percentage—

Shown by symbol size

0 to 25

26 to 50

51 to 80

EXPLANATION

[This explanation shows all possible symbols in order to maintain consistency between this figure 

and similar figures in this report, but not all symbols appear in each figure. The absence of a symbol 

in any individual figure is intentional and means that it does not apply to that individual figure.]

River—Arrow shows direction of flow

PinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth ParkPinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth Park

PinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth ParkPinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth Park

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

A. Total lead concentration, period of record

C. Total lead concentration, 2009–18 D. Total lead load, 2009–18

B. Total lead load, period of record

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Figure 14. Statistical likelihood and magnitude of change in flow-normalized total lead concentrations and loads over the period 

of record and water years 2009–18 for sites in the Spokane River watershed, northern Idaho. Sites are shown in figure 1. Statistical 

likelihoods are defined in table 4. Period of record is defined for each site and constituent in Table 3. Diagram is not to scale.
38 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

Nutrients

The WRTDS and WRTDS_K model results indicate 

variable trends in total phosphorus over the period of record. 

Figure 15 shows the WRTDS_K annual mean concentrations and annual total loads and the WRTDS flow-normalized 

annual mean concentrations and annual total loads for select 

sites (SFCDR near Pinehurst, CDR near Harrison and Spokane 

River below lake outlet; complete results are in appendix 1). 

Over the period of record, increases in total phosphorus concentrations and loads occurred at SFCDR and Pinehurst and 

CDR near Harrison through approximately 2010, followed by 

decreases. Decreases in the Spokane River below lake outlet 

occurred throughout the period of record, although the record 

extended only from WY 2003 to 2018, whereas records from 

the other two sites extended from the 1990s to 2018 (fig. 15).

In the entire study area, trends in total phosphorus for 

flow-normalized concentrations and loads over the period 

of record were variable (Zinsser, 2020; fig. 16). Two sites, 

SFCDR near Pinehurst and CDR near Harrison, had “likely 

up” trends in total phosphorus concentration of 51 percent 

(13 μg/L) and 19 percent (2.7 μg/L), respectively. One site, 

SFCDR at Smelterville, had a “somewhat likely up” trend of 

22 percent (6.3 μg/L). One site, Spokane River below lake 

outlet, had a “likely down” trend of 25 percent (-1.9 μg/L). 

Canyon Creek and SFCDR at Kellogg had “somewhat likely 

down” trends, and there were multiple sites where downward 

trends were “about as likely as not” (SFCDR at Elizabeth 

Park, NFCDR at Enaville and St. Joe River at Ramsdell). The 

flow-normalized load trends were similarly variable. One 

site, SFCDR near Pinehurst, had a “likely up” trend in total 

phosphorus loads of 68 percent (8 metric tons). SFCDR at 

Smelterville and CDR near Harrison, had “somewhat likely 

up” trends of 25 percent (3.1 metric tons) and 11 percent (6.7 

metric tons), respectively. One site, Spokane River below lake 

outlet, had a “likely down” trend of 20 percent (-9.6 metric 

tons). St. Joe River at Ramsdell had a “somewhat likely down” 

trend (17 percent, -16 metric tons). Trends at the remaining 

sites were “about as likely as not.” However, it is critical to 

note that the period of record varied widely, and therefore 

direct comparison of trends was hampered by the mismatch 

between record lengths due to sparse underlying data. The 

SFCDR near Pinehurst model was by far the longest, encompassing WYs 1990–2018; the records at all the other sites were 

substantially shorter, with start dates ranging between WY 

1998 (NFCDR at Enaville) and WY 2006 (SFCDR at Kellogg; 

Zinsser, 2020). 

Contrary to the period of record, the total phosphorus 

trends in flow-normalized concentrations and loads during WYs 2009–2018 were either uncertain or down at all 

sites (Zinsser, 2020; fig. 16). This is logical given the shape 

(non-monotonic) of the WRTDS results (fig. 16) and points 

to one of the benefits of using the WRTDS approach because 

other models (for example, LOADEST) cannot detect nonmonotonic trends. Four sites (NFCDR at Enaville, Canyon 

Creek, SFCDR near Pinehurst, and Spokane River below 

lake outlet) had “likely down” trends in total phosphorus 

concentrations, with the decreases ranging from 12 percent 

(-5.1 μg/L and -0.79 μg/L) at SFCDR near Pinehurst and 

Spokane River below lake outlet, respectively) to 23 percent (-1.4 μg/L) at Canyon Creek. Two sites had “somewhat 

likely down” trends (SFCDR at Kellogg and St. Joe River at 

Ramsdell). Downward trends in total phosphorus concentrations were “about as likely as not” for the remaining sites 

(SFCDR at Elizabeth Park, SFCDR at Smelterville, and CDR 

near Harrison). The flow-normalized load trends were similar. 

Three sites (NFCDR at Enaville, SFCDR near Pinehurst, and 

St. Joe River at Ramsdell) had “likely down” trends, with load 

decreases ranging from 15 percent (-14 metric tons) at St. Joe 

River at Ramsdell to 19 percent (-4.8 metric tons) at SFCDR 

near Pinehurst. Two sites, CDR near Harrison and Spokane 

River below lake outlet, had modest “somewhat likely down” 

trends with decreases around 10 percent. At the remainder 

of the sites, downward trends were “about as likely as not” 

(Zinsser, 2020).

The slope confidence intervals for the total phosphorus 

load trends help to illustrate differences between earlier and 

later time periods by standardizing the timeframe for comparison (fig. 10). Tributary and upstream sites (Canyon Creek, 

Ninemile Creek and SFCDR at Elizabeth Park) had slopes 

near 0 for both WYs 2002–09 and WYs 2009–18. Slopes were 

positive in WYs 2002–09 and negative in WYs2009–18 for 

downstream sites (SFCDR near Pinehurst, NFCDR at Enaville 

and SCDR near Harrison; fig. 10). This reversal in trend direction suggests that some mechanism(s) increased total phosphorus loading at downstream sites during WYs 2002–09, and 

then either the same or different mechanism(s) decreased total 

phosphorus loading at these same sites during WYs 2009–18.

Modeling results for orthophosphate were limited by a 

high number of censored samples at all sites; consequently, 

WRTDS and associated likelihood modeling could only be 

completed for three sites–SFCDR near Pinehurst, CDR near 

Harrison, and St. Joe River at Ramsdell (table 3; Zinsser, 

2020). Over the period of record, flow-normalized orthophosphate concentrations were “likely up” in SFCDR near 

Pinehurst (55 percent, 5.5 μg/L) and CDR near Harrison (78 

percent, 1.5 μg/L). Flow-normalized orthophosphate loads 

were also up at these sites, 40 percent (1.6 metric tons) and 

81 percent (4.3 metric tons), respectively. At St. Joe River at 

Ramsdell, a trend in concentrations was “about as likely as 

not” and a trend in loads was “somewhat likely up” (18 percent, 3 metric tons; Zinsser, 2020).

However, trends for WYs 2009–18 were largely opposite the period of record trends (Zinsser, 2020). At CDR near 

Harrison, flow normalized orthophosphate concentrations and 

loads were “likely down” with a 23 percent decrease (-1.0 

μg/L) in concentration and a 13 percent decrease (-1.4 metric 

tons) in load. At SFCDR near Pinehurst, concentrations were 

“somewhat likely down” (4.1 percent, -0.61 μg/L), although 

loads were “somewhat likely up” (13 percent, 0.65 metric 

tons). Trends in flow-normalized orthophosphate concentration and loads were “about as likely as not” during WYs 

2009–2018 at St. Joe River at Ramsdell (Zinsser, 2020).
Results 39

Changes in orthophosphate concentrations and loads were 

inconsistently related to changes in total phosphorus loads 

and concentrations. For example, although total phosphorus 

and orthophosphate concentrations and loads all increased at 

SFCDR near Pinehurst and CDR near Harrison over the period 

of record, increases in orthophosphate concentrations were 

equal to only about half of the total phosphorus concentration increases at both sites, and orthophosphate load increases 

were equal to a lesser fraction of the load increases. The 

relationships were even less consistent during WYs 2009–18, 

with changes in orthophosphate concentration and load at 

SFCDR near Pinehurst equal to only a small fraction (12–14 

percent) of the total phosphorus changes, and orthophosphate 

loads were trending upwards while total phosphorus loads 

were trending down. At CDR near Harrison, change in orthophosphate concentration was equal to change in total phosphorus concentration, but the trend was “about as likely as not.” 

The likely decrease in orthophosphate load was equal to only 

1990 1995 2000 2005 2010 2015

20

30

40

50

10

15

20

25

5.5

6.0

6.5

7.0

7.5

8.0

Total phosphorus concentration, in micrograms per liter

1990 1995 2000 2005 2010 2015

10

20

30

40

50

100

150

30

40

50

60

70

Total phosphorus load, in metric tons per year

WRTDS_K annual mean concentration 

WRTDS flow-normalized annual mean concentration

WRTDS_K annual total load

WRTDS flow-normalized annual total load

EXPLANATION EXPLANATION

Water year Water year

South Fork Coeur d’Alene River near Pinehurst

Spokane River below lake outlet

Coeur d’Alene River near Harrison

South Fork Coeur d’Alene River near Pinehurst

Spokane River below lake outlet

Coeur d’Alene River near Harrison

Figure 15. Total phosphorus annual mean concentrations and annual total loads from Weighted Regressions on Time, Discharge 

and Season with Kalman filtering (WRTDS_K) and flow-normalized annual mean concentrations and annual total loads from Weighted 

Regressions on Time, Discharge and Season (WRTDS) for select sites in the Spokane River watershed, northern Idaho, water years 

1990–2018. Sites are shown in figure 1. Abbreviations: WRTDS, Weighted Regressions on Time, Discharge and Season; WRTDS_K, 

Weighted Regressions on Time, Discharge and Season with Kalman filtering.
40 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

10 percent of the somewhat likely decrease in total phosphorus 

load. Thus, although the relationships between total phosphorus and orthophosphate changes in the study area were 

complex, changes in orthophosphate concentrations and loads 

were not consistently driving the changes in total phosphorus 

concentrations and loads.

Total nitrogen models and trend analyses were limited by 

the high number of censored values and the fact that there was 

no systematic total nitrogen sampling in the study area before 

WY 2003. For the seven sites with model results (table 3; 

Zinsser, 2020), flow-normalized total nitrogen concentration 

trends were “likely down” during both the period of record 

and WYs 2009–18 at all but St. Joe River at Ramsdell, which 

was “somewhat likely down” over the period of record. 

Decreases in total nitrogen concentration during the period 

of record ranged from 16 percent (-53 μg/L) at SFCDR near 

Pinehurst to 44 percent at NFCDR at Enaville (-33 μg/L) and 

Spokane River below lake outlet (-61 μg/L). Flow-normalized 

total nitrogen load trends were “likely down” during both 

the period of record and WYs 2009–18 at all but two sites, 

SFCDR at Smelterville and SFCDR near Pinehurst, which 

were “somewhat likely down” during the period of record. 

Total nitrogen load decreases during the period of record 

ranged from 12 percent (-15 metric tons) at SFCDR near 

Pinehurst to 41 percent (-333 metric tons) at the Spokane 

River below lake outlet (Zinsser, 2020).

Likelihood descriptor—Shown by 

symbol shape and color

Likely up

Somewhat likely up

About as likely as not

Somewhat likely down

Likely down

No model

Magnitude of change, in percentage—

Shown by symbol size

0 to 25

26 to 50

51 to 80

EXPLANATION

[This explanation shows all possible symbols in order to maintain consistency between this figure 

and similar figures in this report, but not all symbols appear in each figure. The absence of a symbol 

in any individual figure is intentional and means that it does not apply to that individual figure.]

River—Arrow shows direction of flow

PinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth ParkSmelterville

Pinehurst

Cataldo

HarrisonKelloggElizabeth Park

PinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth ParkPinehurstSmelterville

Cataldo

HarrisonKelloggElizabeth Park

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

Below lake outlet

Ramsdell

A. Total phosphorus concentration, period of record

C. Total phosphorus concentration, 2009–18 D. Total phosphorus load, 2009–18

B. Total phosphorus load, period of record

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Coeur d’Alene River

St. Joe River

Spokane River Lake Coeur d’Alene

North Fork

Coeur d’Alene

River

South Fork Coeur d’Alene River

Pine Creek

Ninemile Creek

Canyon Creek

Figure 16. Statistical likelihood and magnitude of change in flow-normalized total phosphorus concentrations and loads over the 

period of record and water years 2009–18 for sites in the Spokane River watershed, northern Idaho. Sites are shown in figure 1.

Statistical likelihoods are defined in table 4. Period of record is defined for each site and constituent in Table 3. Diagram is not to scale.
Results 41

Spatial Patterns in Load Sources

South Fork Coeur d’Alene River

Thus far, discussion of the modeling results has focused 

on flow-normalized concentrations and loads, which are wellsuited for identifying long-term trends. However, looking at 

year-to-year variations in the estimated loads and the incremental loads from upstream to downstream can be helpful for 

identifying mechanisms of transport, evaluating the relative 

load contributions from different source areas, and determining how these may or may not vary on a year-to-year basis. 

To this end, incremental loads for the SFCDR and main-stem 

CDR were calculated using the WRTDS_K annual total load 

estimates and are shown in figures 17 and 18. An incremental 

load represents the load added to a river in an upstream-todownstream reach that ends with a sampling site. This was 

calculated by subtraction; the upstream site load (if present–

some reaches start in headwaters) was subtracted from the 

downstream site load. Negative loads indicate that a constituent had a net loss in a reach, which could occur through deposition, biological uptake, adsorption, losses to groundwater, or 

by other processes. Also note that because the period of record 

necessarily varies by site (see table 3), incremental loads for 

each constituent were calculated to include as many sites as 

possible for as long as possible. Thus, not all sites were used 

for each constituent and longer records were truncated in some 

case for comparability across sites. Additionally, some constituents (for example, nitrogen and orthophosphate) have fewer 

increments based on lack of availability of underlying data.

Figure 17 shows incremental loads in the SFCDR for 

each constituent. Some general observations can be made. As 

total and dissolved cadmium and zinc loads have decreased 

over time, the proportional load from each site has remained 

similar. That is, because metal loads have decreased at each 

site, the relative load contribution of each reach to the overall 

SFCDR has remained about the same although the absolute 

loads have decreased. For total and dissolved zinc and cadmium, the overall biggest contributing segment to the SFCDR 

loads was the SFCDR between Elizabeth Park and Pinehurst. 

Dissolved lead losses occurred in most years in the SFCDR 

reach between the confluence of Canyon and Ninemile Creeks 

with the SFCDR at Elizabeth Park. This reach was also the 

biggest contributor to total lead loads in most years. Total metals loads were biggest during high streamflow years, including 

WYs 2007, 2008, 2011, and 2017, but dissolved metal loads 

were less affected by high streamflow years (fig. 17).

The contribution of different SFCDR reaches to the total 

phosphorus load at SFCDR near Pinehurst varies by year 

(fig. 17). Generally, the SFCDR above Elizabeth Park (which 

includes about two thirds of the total watershed area), the 

reach between Elizabeth Park and Smelterville (where the 

Central Impoundment Area is located), and the reach between 

Smelterville and Pinehurst (where the Smelterville and Page 

wastewater treatment facilities are located) each contribute 

roughly one third of the total phosphorus load, but this varies 

by water year. Total phosphorus loads were biggest during 

high streamflow years such as WYs 2002, 2008, 2011, and 

2017, but these years were not associated with consistently 

bigger contributions from any particular reach. This lack of 

consistency suggests that runoff-associated sources can be 

important to each of these reaches during a high streamflow 

year but are not necessarily important during every high 

streamflow year. However, the SFCDR above Elizabeth Park 

consistently contributed relatively lower total phosphorus 

loads during low streamflow years, while the Elizabeth Park to 

Smelterville and Smelterville to Pinehurst reaches contributed 

more. This pattern is consistent with expected phosphorus 

loads from the Central Impoundment Area and the wastewater 

treatment facilities, both of which would be expected to contribute relatively steady total phosphorus loads year-round and 

year-to-year. Total nitrogen loads could only be calculated for 

a few sites on the SFCDR. Generally, about half of the total 

nitrogen load was from the SFCDR above Elizabeth Park, and 

the other half came from the reach between Smelterville and 

Pinehurst (fig. 17).

Coeur d’Alene River

The relative contributions of the NFCDR, SFCDR, and 

main-stem CDR to the total loads in the CDR near Harrison 

are shown in figure 18. Despite contributing about 70 percent 

of the streamflow to the CDR, the NFCDR contributed only 

minor metal loads (less than 10 percent). The SFCDR has 

been the dominant source of dissolved zinc and cadmium 

(more than 50 percent) throughout the period of record, but 

the proportion of these loads that the CDR main stem contributes has increased over time. Note that the dissolved zinc and 

cadmium loads from the main-stem CDR are not increasing; 

they are simply proportionally more important to the total load 

at CDR near Harrison as loads from the SFCDR decrease. In 

contrast, the SFCDR was the dominant source of total zinc and 

cadmium until approximately WY 2005. Since then, the CDR 

main stem has contributed more than 50 percent of the total 

zinc and cadmium loads in many water years. The CDR main 

stem remained the dominant source of total and dissolved lead, 

generally contributing greater than 75 percent of the total load. 

While the SFCDR was a significant source of the total lead 

load (greater than 25 percent) in some low water years prior to 

WY 2000, its contribution has decreased since then (fig. 18).

Although the NFCDR likely contributes some orthophosphate load to the CDR, there were too many censored values 

to construct a model for this parameter at this site. So, within 

this analysis, the load from the NFCDR was 0 (fig. 18). Of the 

measurable orthophosphate loads, about half derive from the 

SFCDR and about half from the main-stem CDR, with contributions from the main-stem CDR tending to be larger during 

high streamflow years (fig. 18). The NFCDR contributed about 

half of the total phosphorus and total nitrogen loads as measured at CDR near Harrison, on average, while the SFCDR 

contributed about 25–30 percent of the total phosphorus and 

total nitrogen loads, respectively. On average, the remainder, 
42 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

about 20–25 percent to the total nitrogen and total phosphorus loads, respectively, were gained in the main-stem CDR. 

However, substantially larger portions of the total phosphorus 

load (up to half) were contributed by the main-stem CDR during high streamflow years such as 2011 and 2017 (fig. 18).

Coeur d’Alene Lake

The relative load contributions of the CDR and the St. 

Joe River to Coeur d’Alene Lake, and the load out of Coeur 

d’Alene Lake to the Spokane River, are shown in figure 19. 

Note that for metals, it is a reasonable assumption that loads 

from the CDR and St. Joe River account for the essentially 

all-metal loading to the lake. For nutrients, however, there 

are likely additional loads from smaller tributaries and the 

lakeshore itself that are not accounted for in this analysis; thus, 

the nutrient loads into and out of the lake represented here do 

not represent a complete mass balance. Likewise, neither the 

metals nor the nutrient comparisons of loads in and loads out 

account for in-lake processes. Virtually all the metal loads 

to Coeur d’Alene Lake came from the SFCDR. The load out 

of Coeur d’Alene Lake via the Spokane River was generally 

equivalent to most of the dissolved zinc load and approximately half of the dissolved cadmium load entering the lake, 

with more exported during higher streamflow years. Generally, 

an amount equivalent to about 50–75 percent of the total 

zinc and cadmium loads into Coeur d’Alene Lake remained 

there; this seemed to be relatively insensitive to interannual 

Lead, total Zinc, dissolved Zinc, total

Nitrogen, total Phosphorus, total

Cadmium, dissolved Cadmium, total Lead, dissolved

2000 2005 2010 2015

2000 2005 2010 2015

2000 2005 2010 2015

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Incremental annual load, in metric tons per year

Reach

Headwaters to Canyon Creek

Headwaters to Ninemile Creek

SFCDR headwaters to Elizabeth Park

SFCDR from Elizabeth Park to Smelterville

Headwaters to Pine Creek

SFCDR from Elizabeth Park to Pinehurst

SFCDR from Smelterville to Pinehurst

Annual total loads at SFCDR near Pinehurst

EXPLANATION

Figure 17. Incremental annual total loads for sites in the South Fork Coeur d’Alene River (SFCDR), northern Idaho, water years 

1999–2018. Load estimates were not available for all sites and constituents for every year. Annual total loads at the downstream-most 

SFCDR site (SFCDR near Pinehurst) are shown with dots.
Results 43

variability in streamflow. The total lead and dissolved lead 

loads flowing out of Coeur d’Alene Lake via the Spokane 

River were low relative to the amount flowing in, although 

more dissolved lead flowed out during high streamflow years 

(fig. 19).

Although the two rivers contributed roughly equal 

amounts of streamflow to the lake, more than half of the total 

nitrogen and orthophosphate load derived from the St. Joe 

River. The Spokane River exported total nitrogen equivalent 

to most of the total nitrogen load entering the lake except 

during high streamflow years, when it exported substantially 

less. Orthophosphate was not detected frequently enough to 

construct a model for the Spokane River below lake outlet, so 

for this analysis all orthophosphate that enters the lake stays in 

it, although it is likely that some net export of orthophosphate 

occurs. For total phosphorus, on average, about half of the 

load derived each from the CDR and St. Joe River. However, 

the CDR tended to contribute more than half during high 

streamflow years (for example, WYs 2008, 2011, and 2017), 

and the St. Joe River tended to contribute more than half during low or average streamflow years. Generally, the Spokane 

River exported total phosphorus equivalent to about 25 percent 

of the total phosphorus load entering the lake; this ratio was 

relatively insensitive to interannual variability in streamflow.

Phosphorus, total Zinc, dissolved Zinc, total

Lead, total Nitrogen, total Orthophosphate

Cadmium, dissolved Cadmium, total Lead, dissolved

2000 2010 2000 2010 2000 2010

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Incremental annual load, metric tons per year

Reach

EXPLANATION

Main-stem Coeur d’Alene River North Fork Coeur d’Alene River South Fork Coeur d’Alene River

Annual total load at Coeur d’Alene River near Harrison

Figure 18. Incremental annual total loads for the South Fork Coeur d’Alene River (SFCDR), the North Fork Coeur d’Alene River 

(NFCDR), and the main-stem Coeur d’Alene River (main-stem CDR), northern Idaho, water years 1994–2018. Load estimates were 

not available for all sites and constituents for every year. Annual total loads at the downstream-most site (CDR near Harrison) are 

shown with dots. SFCDR represents total loads in the SFCDR near Pinehurst. NFCDR represents total loads in the NFCDR at Enaville. 

Main-stem CDR loads represent total loads at CDR near Harrison minus loads from the SFCDR and NFCDR.
44 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

Discussion

The analyses presented in this report are intended to 

explore the current state of water quality in the study area and 

trends therein over the previous 30 years, specifically focusing on concentrations and loads of select metals and nutrients 

and the effects of remedial actions. Despite the focus on select 

constituents, water-quality trends in the study area are an 

expansive topic, and the results presented here rely on a large 

amount of data and supporting statistical analyses. As such, 

to better focus the discussion, this section is framed around 

a series of key questions regarding important constituents, 

patterns, and trends in the study area. This is not an exhaustive examination of the underlaying data and trends, but it 

does aim to address some major themes based on previous 

research and current topics in the study area. Furthermore, 

the study presented here is fundamentally a trends analysis; it 

illuminates patterns in water quality over 30 years but cannot 

directly identify the mechanisms responsible for those trends. 

Instead, this section relies on the trend analysis in conjunction 

with the body of existing technical literature describing constituent sources and mechanisms of transport to draw conclusions about change in the study area.

Water year

Reach

Coeur d’Alene River St. Joe River

Annual total load at Spokane River below lake outlet

EXPLANATION

2004 2008 2012 2016 2004 2008 2012 2016 2004 2008 2012 2016

0

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Incremental annual load, metric tons per year

300

Phosphorus, total Zinc, dissolved Zinc, total

Lead, total Nitrogen, total Orthophosphate

Cadmium, dissolved Cadmium, total Lead, dissolved

Figure 19. Annual total loads into and out of Coeur d’Alene Lake, northern Idaho, water years 2005–18. Annual total loads from the 

Coeur d’Alene River (CDR) represent annual total loads at CDR near Harrison. Annual total loads from the St. Joe River represent 

annual total loads at the St. Joe River at Ramsdell. Annual total loads out of Coeur d’Alene Lake represent annual total loads in the 

Spokane River below lake outlet and are shown with dots.
Discussion 45

Metals

First, have concentrations and loads of metals decreased 

since WY 1990? If so, what is the level of statistical confidence 

in these trends? And, finally, sharp decreases in metals concentrations were observed from the 1990s through the early 

2000s, but these decreases appeared to taper off in the 2010s 

(Clark and Mebane, 2014)–have improvements continued in 

WYs 2009–18?

Total and dissolved zinc and cadmium and total lead 

concentrations and loads have decreased with high statistical 

likelihood (“likely down” or “somewhat likely down” trends) 

at most mining-affected sites across the study area over the 

period of record (the last 13–29 years; figs. 9, 12, and 14). 

One notable exception was the total lead load in the CDR near 

Harrison, which had a “somewhat likely up” trend over the 

period of record although dissolved zinc and cadmium at this 

site were “likely down.” Furthermore, decreases in total and 

dissolved zinc and cadmium and total lead loads and concentrations persist with high statistical likelihood (“likely down” 

or “somewhat likely down” trends) at most sites over the most 

recent decade analyzed, WYs 2009–18, although the absolute 

magnitude of the decreases is smaller relative to the period 

of record. However, total lead load decreases at three sites, 

SFCDR at Elizabeth Park, SFCDR at Kellogg, and CDR near 

Harrison were “about as likely as not” during WYs 2009–18. 

The decreasing trends for most sites in WYs 2009–18 are most 

readily apparent in the flow-normalized concentrations and 

loads, where the variability driven by differences in annual 

streamflow is dampened (figs. 8, 11, and 13). By standardizing the trend periods (WYs 1999–2009 and WYs 2009–18) 

and looking just at the slope of the load trends, it is clear that 

although the absolute magnitude of the load decreases in 

WYs 2009–18 are smaller, the rate of the decreases is generally similar between the two periods (fig. 10). Thus, based on 

the analyses presented in this report, the concentrations and 

loads of key constituents in the study area have decreased with 

high statistical likelihood over the past 13–29 years (period of 

record), and have continued to decrease with high statistical 

likelihood at most sites during WYs 2009–18.

Next, how have remedial actions influenced these changes 

in concentrations and loads?

 Although this trend analysis cannot specifically ascribe 

causality for trends, it can rely on existing documentation of 

metal sources, fate, and transport mechanisms to understand 

if observed trends are congruent with the likely impacts of 

remedial activities. Previous works have developed detailed 

conceptual models describing source, fate, and transport of 

metals in the Bunker Hill Superfund Site (URS Grenier, Inc., 

and CH2M HILL, 2001; CH2MHILL, 2006 and 2010a). In the 

SFCDR and tributaries, zinc, cadmium, and lead in primary 

sources such as adit and seep drainage, tailings and waste 

rock occur in approximately 1,088 source areas throughout 

the Bunker Hill Superfund Site. From these primary sources, 

zinc, cadmium, and lead are readily mobilized and transported 

in particulate and dissolved forms in surface water and in 

dissolved form in groundwater (URS Grenier, Inc., and CH2M 

HILL, 2001). Moreover, surface water and groundwater readily exchange in multiple areas of the Bunker Hill Superfund 

Site; for example, areas with bedrock constrictions force 

groundwater into rivers, and areas with bedrock expansions 

and a bigger alluvial aquifer promote surface water infiltration into groundwater. Such exchanges occur throughout 

the SFCDR watershed and have been specifically studied in 

Canyon Creek, the SFCDR near Osburn, and the SFCDR near 

Smelterville (Barton, 2002; CH2MHILL, 2009a–b; Zinsser, 

2019). Secondary sources of metals therefore include soils, 

sediment, floodplain deposits, groundwater, and surface water 

that occur throughout the CDR watershed.

Numerous and varied actions by the EPA have been 

implemented across the Bunker Hill Superfund Site since the 

early 1990s. For example, remedial actions in the SFCDR 

watershed have included (but are not limited to) the removal 

of contaminated materials from streams and floodplains, 

consolidation of source materials, closure of waste repositories, demolition of mine and mill structures, remediation 

of specific mine sites, capping of the Central Impoundment 

Area, upgrades to the Central Treatment Plant, hillside erosion 

control, revegetation and riparian planting, and remediating the railroad right of way and subsequently opening the 

Trail of the Coeur d’Alenes (U.S. Environmental Protection 

Agency, 2012a). Additional cleanup activities have been 

implemented by other entities (including by the Bureau of 

Land Management in Pine Creek and by various site owners 

in Canyon Creek) and focused on removing contaminated 

materials from streams and proximal land surfaces (U.S. 

Environmental Protection Agency, 2012a).

The large and statistically likely decreases in total and 

dissolved cadmium, zinc, and lead concentrations and loads 

at sites throughout the SFCDR over the period of record are 

consistent with the anticipated effects of the many remedial actions that have occurred in the watershed during this 

time. For example, erosion of particulate lead, cadmium, and 

zinc during high streamflow from readily accessible mining wastes contributed to high loads during runoff events. 

Removal of these sources from streams and floodplains were 

among the earliest remedial activities throughout the Bunker 

Hill Superfund Site in the 1990s and early 2000s (U.S. 

Environmental Protection Agency, 2012a); this aligns with 

the period of steepest declines in particulate metal loads in 

SFCDR and tributary sites. Similarly, dissolved metal concentrations in surface water would be expected to decline steeply 

as these source materials were removed, and then continue 

to decline less steeply as groundwater concentrations gradually decrease over time in response to fewer source inputs. 

Again, this aligns with the concentration trends observed for 

dissolved metals in SFCDR and tributary sites. Ultimately, the 

strong and pervasive downward trends in total and dissolved 

metals in the SFCDR and tributary sites suggest that the remedial actions to remove primary materials from streams and 

floodplains and contain these materials in designed, intentional 

repositories have decreased cadmium and zinc loads and 

concentrations.
46 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

In contrast to the high gradient SFCDR system, the 

main-stem CDR system is highly complex, comprising 

approximately 30 low-gradient, meandering river miles in fine 

grained substrate that are hydraulically connected to 12 shallow lateral lakes, thousands of acres of wetlands, and extensive floodplains (CH2MHILL, 2010a). Because of the nature 

and complexity of the river system in the main-stem CDR, 

the conceptual models for constituent transport in this area 

differ from those higher in the Bunker Hill Superfund Site. 

Most importantly, the major source of metals is contaminated 

sediments. The Cataldo Flats area, located at the confluence 

of the NFCDR and SFCDR, was the site of the largest tailings 

impoundment in the valley, and lead-rich sediment remains 

widely dispersed through the main-stem CDR system (U.S. 

Environmental Protection Agency, 2012a). These particulate 

metals are primarily mobilized by erosion from riverbanks 

and the channel bottom during high flow events; floodplain 

sediments are thought to be a relatively unimportant source of 

lead (CH2MHILL, 2010a). Contaminated sediments are also a 

source of dissolved metals within the main-stem CDR system. 

Oxic, suboxic, and anoxic zones can develop seasonally in the 

deeper riverbend, riverbank, marsh, wetland and lateral lakes 

zones. Under anoxic conditions, iron oxyhydroxide dissolves 

and can release adsorbed lead, zinc, and cadmium back into 

the water column. Organic matter can also adsorb and release 

zinc and cadmium, and lead complexed on organic material 

can be highly mobile (URS Grenier, Inc., and CH2M HILL, 

2001; CH2MHILL, 2010c). Due to the complexity of contamination in the main-stem CDR, including the potential for 

recontamination from upstream sources, remedial activities in 

this area over the past 20 years have been focused on gaining 

an in-depth understanding of processes in this area and have 

included only limited source removals associated with popular 

recreation areas and construction of the Trail of the Coeur 

d’Alenes (U.S. Environmental Protection Agency, 2012a).

Given the nature of contaminant transport and relative lack of removal activities in the main-stem CDR, it is 

unsurprising but important that trends at CDR near Harrison 

vary somewhat from trends observed higher up in the watershed. Because the SFCDR is the source of the majority of 

the dissolved zinc and cadmium loads in CDR near Harrison 

(fig. 18), this site also experienced strong downward trends 

for these constituents, driven by upstream remedial actions. 

In contrast, the CDR main stem itself is the source of the 

majority of the total and dissolved lead at CDR near Harrison. 

Because contaminated sediments in the main-stem CDR have 

yet to be systematically addressed by widespread remedial 

activities in this area, it is logical that total and dissolved 

lead loads did not trend down during the period of record. So 

again, the trends observed in metals in the main-stem CDR 

are congruent with known sources of metals and mechanisms 

of transport in this area and are consistent with the history of 

remedial actions.

Finally, it is beyond the scope of this report to address 

how metals may transform in or transit through Coeur d’Alene 

Lake and whether these processes may be changing over time. 

However, it is important to note that total and dissolved metal 

concentrations and loads in the Spokane River below lake 

outlet show large and statistically likely decreases over the 

period of record. Because these trends are similar in nature 

and timing to trends through the CDR watershed, this synchrony suggests that the water-quality improvements in the 

CDR, driven by extensive remedial activities, are also improving water quality in the Spokane River downstream of Coeur 

d’Alene Lake.

Can changes be attributed to specific remedial actions? 

How do the observed changes in AWQC ratios, concentrations, and loads compare to specific cleanup goals?

 Despite the probable link between the metal trends and 

remedial actions in general, the method of trends analysis 

used here cannot detect step changes that may be associated 

with specific remedial actions. This is partly because so many 

actions have occurred simultaneously across the Bunker Hill 

Superfund Site, so the effects of each have compounded to 

yield large decreases in metals loads and concentrations at 

each monitoring site. This effect is especially apparent in the 

downstream-most sites (for example, SFCDR near Pinehurst), 

which experienced the largest load and concentration percent 

changes due to the additive improvements of each upstream 

site. Moreover, although the data collection efforts in the study 

area spanned many years, the sample frequency per year was 

relatively low (generally 4–6); this low frequency, combined 

with interannual streamflow variability, makes step changes 

associated with individual remedial actions harder to detect in 

the data. Most importantly though, WRTDS is fundamentally 

a statistical smoothing method that will inherently have a 

tendency to make step trends appears smoother than they are. 

In sum, it is possible that a different analysis approach could 

resolve discrete water-quality changes from specific actions, 

but the analyses presented here are not well-suited to detect 

such changes.

Likewise, step changes are not discernible in the AWQC 

ratios presented for the 20 WYs 2009–18 water-quality 

monitoring sites (figs. 3–5). Beyond the issues presented 

above, AWQC ratios can also vary widely at a given site as 

the underlying constituent concentrations and sample hardness 

vary with streamflow. For example, lead transport tends to be 

highest during spring runoff or flood streamflows when hardness values are also at their lowest, resulting in higher AWQC 

ratios relative to baseflow conditions. The AWQC ratios for 

a single site therefore can vary widely across the water year, 

which could also obscure step changes. However, for some 

sites with longer continuous data records such as SFCDR 

at Elizabeth Park and SFCDR near Pinehurst, decreases in 

dissolved zinc and dissolved cadmium AWQC ratios are only 

apparent after WY 1998 (figs. 3–4). This may indicate it took 

multiple remedial actions, and multiple seasons, for improvements in the AWQC ratios to become pronounced enough to 

be discernible from the variability induced by seasonal and 

annual streamflows.
Discussion 47

Although there are strong, downward trends in most metals at most sites over the period of record, direct comparisons 

of these decreases to cleanup goals are limited because specific, quantified cleanup goals are rare in the various Records 

of Decision. The 2002 Record of Decision for the Bunker Hill 

Superfund Site included several specific, comparable interim 

benchmarks for ecological receptors (U.S. Environmental 

Protection Agency, 2002). One benchmark for Canyon Creek 

aimed to reduce dissolved metal loading by 50 percent. Over 

the period of record at this site (WYs 1999–2018), dissolved 

cadmium loads decreased 50 percent, dissolved lead loads 

decreased 61 percent, and dissolved zinc loads decreased 

40 percent (Zinsser, 2020). A benchmark for the main-stem 

Ninemile Creek was to reduce acute AWQCs ratios to less 

than 20; median chronic AWQC ratios (which are more stringent than acute for cadmium and lead) for WYs 2014–18 were 

19, 1.3, and 16 for dissolved cadmium, dissolved lead, and 

dissolved zinc (respectively; table 7). Although limited, these 

comparisons provide another means to indicate the magnitude 

of improvement in zinc and cadmium concentrations and loads 

in the study area over the last several decades.

Next, are spatial patterns in metal loading changing (or 

not) across study area? Is the SFCDR still the main source of 

dissolved zinc and cadmium? Is the main-stem CDR still the 

main source of total and dissolved lead? 

The majority of the dissolved zinc and cadmium loads in 

the CDR near Harrison still derive from the SFCDR (generally 

greater than 75 percent; fig. 18). However, as dissolved zinc 

and cadmium loads from the SFCDR have decreased over the 

period of record, this has impacted the relative contributions 

of different sources areas in the system. For example, although 

dissolved zinc and cadmium loads from the main-stem CDR 

have not changed in magnitude, their relative contribution to 

the total load at CDR near Harrison has become bigger. The 

main-stem CDR has continued to contribute the majority of 

the total and dissolved lead loads (generally greater than 75 

percent; fig. 18).

A few other notable spatial patterns in constituent transport are evident in the incremental annual total load analyses. First, for most sites in the upper CDR watershed (above 

SFCDR near Pinehurst), strong decreasing trends in total lead 

loads and concentrations correspond with remedial actions. 

One notable exception, however, is the SFCDR at Elizabeth 

Park and the next downstream site, SFCDR at Kellogg 

(fig. 14). The lack of strong trends, down or otherwise, at these 

sites suggests there is still an active total lead source upstream. 

The upstream reach includes Osburn Flats, which is a recognized source of tailings that continues to be addressed through 

remedial activities. In the early 1900s, a plank-and-pile dam 

was built in this relatively broad, flat part of the valley to 

impound tailings; the dam was subsequently breached multiple 

times during high streamflows, resulting in substantial downstream transport of tailings. Nonetheless, large quantities of 

tailings remain in the valley (U.S. Environmental Protection 

Agency, 2012a). The total lead concentration and load trend 

data for the sites immediately downstream of this area suggest 

that Osburn Flats may be a continuing source of total lead in 

the SFCDR.

Trends in concentrations and loads and incremental load 

patterns in the main-stem CDR show some important differences compared to those in the SFCDR. Sampling access to 

this area is limited to a few bridges or boat-based sampling; 

consequently, long-term monitoring data are spatially sparse, 

which limits the resolution of this analysis. Nonetheless, some 

patterns are apparent. In the main-stem CDR, concentrations of total lead have decreased over the period of record, 

but loads either have “somewhat likely down” trends (WYs 

2009–18) or are increasing (period of record; fig. 14). The 

improvements in main-stem CDR total lead concentrations 

may be due to downstream propagated improvements from the 

SFCDR. In contrast, loads have not improved because high 

streamflow events that mobilize substantial quantities of total 

lead-rich sediment from within the main-stem CDR itself are 

the primary drivers of the total lead load, and these sources 

have not yet been remediated. It is, however, unclear why total 

lead loads increased in WYs 1999–2009 but decreased in WYs 

2009–18 (fig. 10). Generally, riverbed sediment characterization in the main-stem CDR suggests that as the river erodes 

deeper into the bed over time, sediment with higher lead concentrations will be accessible (CH2MHILL, 2010d). However, 

although specific reaches are known to have eroded doing 

specific high streamflow events, it is not clearly understood 

whether the main-stem CDR overall has been eroding over the 

past 20 years (CH2MHILL, 2010b). Thus, it is possible that 

higher lead loads during WYs 1999–09 were associated with 

increased erosion in the main-stem CDR but more data are 

needed to support this hypothesis.

Nutrients

As described in this report’s Introduction, nutrients 

are not constituents of concern under any of the Records of 

Decision but are a current concern in the study area due to 

their potential impact on the trophic status of Coeur d’Alene 

Lake. In contrast to the metals, datasets for total phosphorus, 

total nitrogen, and orthophosphate were generally sparser and 

had more variable trends. These constituents also have less 

prior research to guide questions on trends and patterns of 

transport in the study area. Nonetheless, some broad questions 

were explored here, but additional data and analysis would 

help to improve understanding of the changes and mechanisms 

driving the trends.

Are there trends in total phosphorus concentrations and 

loads in the study area? Where and over what time scales? 

What is the level of statistical confidence in these results? 

What can and cannot be inferred about sources, processes and 

spatial patterns in loading from these results?
48 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

 Generally, the period of record total phosphorus results 

were striking for having several sites with “likely up” or 

“somewhat likely up” trends (SFCDR at Smelterville, SFCDR 

near Pinehurst and CDR near Harrison), whereas the WYs 

2009–18 results were striking for the opposite reason–these 

same sites had “likely down,” “somewhat likely down,” or “as 

likely as not” trends (fig. 16). The slope analysis helps resolve 

these trends, showing that total phosphorus load changes were 

positive at SFCDR at Smelterville, SFCDR near Pinehurst, 

NFCDR at Enaville, and CDR near Harrison from WY 2002 to 

2009 and negative or close to 0 at each of these sites for WYs 

2009–18 (fig. 10). The general (although not perfect) agreement between concentration and load trends and the analysis 

of spatial patterns in loading suggests that the major sources of 

total phosphorus are most important during high streamflows. 

The lack of consistent trends across study area, particularly 

in the upper SFCDR, NFCDR, and St. Joe River, indicate 

that regional mechanisms such as atmospheric deposition or 

changes in forestry practices are unlikely to be driving phosphorus trends. Similarly, it is improbable that geologic sources 

of phosphorus would affect spatially heterogeneous, decadalscale trends, and the Belt Supergroup rocks that underlie much 

of study area have low phosphorus content (Harrison and 

Grimes, 1970; Lewis and Frost, 2005). Furthermore, important 

albeit subtle differences in the magnitude and direction of the 

trends in the SFCDR sites and CDR near Harrison suggest that 

phosphorus trends at these sites may be responding to fundamentally different drivers.

With respect to the SFCDR sites, the load increase in 

SFCDR near Pinehurst in the 2000s was similar to the load 

increase in SFCDR at Smelterville, indicating that change in 

the latter may have driven the trend in SFCDR near Pinehurst 

over this period. However, the biggest change in SFCDR 

near Pinehurst occurred from WY 1990 to 1999, when there 

was no data from SFCDR at Smelterville, and the decrease in 

SFCDR near Pinehurst in WYs 2009–18 was much stronger 

and larger than the decrease in SFCDR at Smelterville over 

the same time period (Zinsser, 2020). Thus, while the total 

phosphorus load from SFCDR at Smelterville likely influences 

trends in SFCDR near Pinehurst to some extent, it is not the 

only control.

There are a variety of known sources of total phosphorus to the SFCDR between Kellogg and Pinehurst. The reach 

between Kellogg and Smelterville, adjacent to the Central 

Impoundment Area, contributes a substantial total phosphorus load via groundwater contributions to the SFCDR. 

Groundwater modeling for WYs 2009–14 shows that this load 

is relatively constant year-to-year, despite interannual variability in streamflow, and is also relatively consistent seasonally, at least for the modelled period (CH2M, 2018). The total 

phosphorus in the groundwater in this reach derives from 

gypsum wastes in the Central Impoundment Area that were 

a byproduct from the phosphoric acid and fertilizer plant in 

Government Gulch. Substantial remediation activities have 

occurred associated with the plant and these wastes since 

the 1990s, including removal, consolidation, and capping of 

wastes that were formerly in the stream channels of several small tributaries to the SFCDR (U.S. Environmental 

Protection Agency, 2012a). It is, however, unexpected that 

removal and consolidation activities in the 1990s would have 

caused loading increases to the SFCDR during the early 2000s 

before leveling off in the 2010s, so it seems unlikely that these 

wastes would be responsible for observed increases.

There are two permitted wastewater treatment systems–

Page wastewater treatment plant and the much smaller 

Smelterville facility–in the reach between Smelterville 

and Pinehurst. Limited data suggest that loads from these 

facilities have remained similar since the early 1990s (Idaho 

Department of Environmental Quality and Coeur d'Alene 

Tribe, 2019). The reach between Kellogg and Pinehurst is 

also relatively urbanized compared to the rest of study area, 

containing several small towns, the I-90 interstate, various 

impervious surfaces, and stormwater systems in addition to the 

mining-related features all within the narrow valley floor. The 

annual load results for this reach suggest that runoff-related 

total phosphorus loads are important during high water years 

(fig. 17). Thus, it is likely that stormwater and other runoffs 

are important (albeit difficult to quantify) contributors of total 

phosphorus to this reach and may have contributed to trends 

over the period of record. For example, remedial actions have 

included substantial paving efforts to isolate contaminated 

road base materials and other efforts to reduce surface erosion 

from mining-related features. While most of the SFCDR is 

forested, the mining impacted and redeveloped areas between 

Kellogg and Pinehurst are heavily concentrated along the 

SFCDR. It is possible that these efforts initially increased 

stormwater runoff to the streams, particularly as revegetation 

efforts began, and have become less important as surface erosion stabilization efforts across the area have taken effect.

Although both SFCDR near Pinehurst and CDR near 

Harrison have “likely up” trends in total phosphorus over 

the period of record (fig. 16), they functionally represent 

the aggregate loads over very different stretches of river and 

are likely responding to different drivers. As described in 

the Results, the shorter period of record results at CDR near 

Harrison are not directly comparable to the longer period of 

record results for SFCDR near Pinehurst because of the difference in record length. There is no discernible trend in NFCDR 

at Enaville over the period of record, and the increase in CDR 

near Harrison (6.7 metric tons) is superficially comparable in 

scale to the increase in SFCDR near Pinehurst (8 metric tons). 

However, the time span represented by each period of record 

is drastically different, with the SFCDR near Pinehurst record 

representing WYs 1990–2018 and the CDR near Harrison 

record representing WYs 1998–2018 (Zinsser, 2020). Total 

phosphorus data were too sparse at CDR near Harrison in 

the 1990s to extend the model back to WY 1991; there was 

only one sample analyzed for total phosphorus between WY 

1993 and 1997. However, over 50 samples were collected in 

calendar years 1991–92 in CDR near Harrison, and multiple 

authors have used these samples to estimate loads previously. 

Woods and Beckwith (1997) estimated annual loads of 22 and 
Discussion 49

10 metric tons in calendar years 1991 and 1992, respectively, 

using FLUX; Wood and Beckwith (2008) later estimated 

33.6 and 10.9 metric tons in calendar years 1991 and 1992, 

respectively, using LOADEST. Although the prior estimates 

vary from each other, both estimates are drastically lower than 

the WRTDS_K (55 metric tons) and WRTDS flow-normalized 

annual loads (61.7 metric tons) calculated here for WY 1999 

(Zinsser, 2020). Water years are different than calendar years, 

but the rough comparison suggests that, during the 1990s, 

the change in load at SFCDR near Pinehurst (approximately 

10 metric tons) can account for only a fraction of the change 

observed in the CDR near Harrison (approximately 20–33 

metric tons). This load disparity suggests that different sources 

of total phosphorus and/or mechanisms of transport are largely 

responsible for trends in the CDR near Harrison.

Despite these data limitations, the load estimates from 

Woods and Beckwith (1997) combined with the WRTDS 

results presented here suggest that the 1990s were evidently 

a period of much bigger phosphorus load increases for CDR 

near Harrison, with more modest increases in the 2000s, and 

declines in recent times (Zinsser, 2020). These broad trends 

are similar to those observed for SFCDR near Pinehurst. 

Furthermore, the increasing trends in CDR near Harrison 

from approximately 1991–2010 are consistent with recent 

analyses by Idaho Department of Environmental Quality and 

Coeur d'Alene Tribe (2019), but because this report incorporated additional years (WYs 2014–18), the decreasing trend 

in WYs 2009–2018 is newly identified here. As described in 

the Metals section of the Discussion, the main-stem CDR is 

a long, low-gradient river connected to a series of shallow, 

productive lateral lakes and wetlands, with water and sediment conveyed between these features and the main stem via 

lateral connecting channels (CH2MHILL, 2010c). Phosphorus 

is not conservative, and it is likely that major transformations 

occur throughout this reach; for example, the main-stem CDR 

adds substantial orthophosphate loads (fig. 18). It is likewise 

notable that the biggest total phosphorus and orthophosphate 

loads in the main-stem CDR occurred during high streamflow 

years, suggesting that floodwaters accessing lateral lakes, 

floodplains, and wetlands may pick up substantial phosphorus 

loads during these years. Alternately, high streamflow years 

are also known to erode and transport substantial quantities 

of particulate lead from the bed of the CDR (Box and others, 

2005; CH2M, 2016), and it is possible that some particulate 

phosphorus load is also stored in and then entrained from the 

bed of the river during these events. Particulate phosphorus 

storage on riverbeds and in floodplains can be important to 

annual phosphorus loads, and phosphorus retained in connected ponds can be an important source of orthophosphate 

(Withers and Jarvie, 2008). However, even if these sources are 

responsible for adding phosphorus to the main-stem CDR during high streamflows, it is unclear why or how the rate of these 

processes would have increased strongly in the 1990s, less 

strongly in the 2000s, and then decreased in the 2010s.

One possibility is that flooding in 1996, which represents 

the second-highest streamflow recorded at CDR near Cataldo 

since 1920 (Box and others, 2005), perturbed the main-stem 

CDR system to make phosphorus more readily available for 

transport. Although there was no systematic study of geomorphic change resulting from the 1996 flood event, the event 

encompassed prolonged, extensive overbank flooding that 

eroded streambank deposits and suspended floodplain soils 

(Box and others, 2005). The prolonged flooding and eventual 

retreat of floodwaters could have either made a substantial 

amount of total phosphorus directly accessible (that is, by 

deposition of phosphorus-rich sediment in the main channel) or created better continual access to the lateral lakes and 

marshes (that is, by scouring out connective channels between 

the main stem and these features). Changes resulting from 

these mechanisms could potentially account for the large 

(albeit anecdotal) increase in total phosphorus load between 

calendar years 1991 and 1992 and WY 1999 and then account 

for reduced increases in the early 2000s as the main-stem CDR 

slowly returned to its previous condition (that is, erosion of the 

high-phosphorus sediments or more limited access to wetlands and marshes). Metal analyses of flood deposit sediments 

associated with a series of floods in the 1990s found that the 

1996 flood was sufficiently large to erode both floodplain 

soils and streambed sediments, whereas smaller floods (more 

readily equivalent to annual spring runoff streamflows) tended 

to primarily mobilize sediment from the streambed (Box and 

others, 2005).

Thus, based on subtle but key differences in phosphorus 

concentrations and loads and innately different environments, 

phosphorus trends at sites in the SFCDR and at the CDR near 

Harrison are likely responding to different processes of phosphorus production and mechanisms of transport. However, 

interpretation of the mechanisms underlying these trends 

remains limited due to the spatial and temporal sparseness of 

the underlying data.

Is there a link between metals and phosphorus in the 

study area? 

Thus far in this report, since the motivation for analyzing metals and nutrients differed, the two types of constituents 

have been considered separately. But as Idaho Department 

of Environmental Quality and Coeur d'Alene Tribe (2019) 

have pointed out, there is some spatial concurrence between 

important sources of metals and nutrients in the SFCDR and 

main-stem CDR. While this is true, the link between metals 

and nutrients seems to be indirect at best. First, as described 

here, the trends for metal concentrations and loads differ 

substantially from those for total phosphorus and orthophosphate, which indicates that governing processes for each differ. 

Second, while there is one identified source of phosphorus 

associated with mining activities (the phosphoric acid wastes 

in the Central Impoundment Area), loading from this source 

has been explicitly estimated (CH2M, 2018; Zinsser, 2019) 

and represents only a small fraction of the phosphorus present in the CDR system. On average, the modeled phosphorus 
50 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

loading from Central Impoundment Area groundwater to the 

SFCDR was about 6.5 metric tons per year in WYs 2009–14 

(CH2M, 2018), whereas the average annual total phosphorus 

load in CDR at Harrison over the same time period was about 

80 metric tons (Zinsser, 2020). Thus, most of the phosphorus 

in the system clearly derives from other sources.

However, there are a variety of ways in which the various and extensive remedial actions across the Bunker Hill 

Superfund Site could indirectly affect phosphorus production 

and loading. For example, widespread paving and redevelopment of lands proximal to the SFCDR could have increased 

impervious surfaces and increased surface runoff, whereas 

remedial actions to revegetate land surfaces and riparian 

areas, mitigate surface erosion, and reduce bank erosion could 

have reduced surface runoff and instream sediment loading. 

Reduced sediment and metal concentrations and loads resulting from remedial actions could have increased water clarity 

and allowed for greater primary productivity, particularly in 

the main-stem CDR (Idaho Department of Environmental 

Quality and Coeur d'Alene Tribe, 2019). There could also 

be some hereto unrecognized connection between high lead 

content and high phosphorus content in sediments stored in the 

main-stem CDR. Thus, while the data presented here suggest 

that the processes governing metal and phosphorus transport 

and the trends therein are fundamentally different, remedial 

actions could be indirectly affecting nutrient trends in a variety of ways.

Topics for Additional Study

While the analyses presented here have characterized a 

series of important trends in concentrations and loads in the 

study area over the last 30 years and attempted to address 

some key themes, there remain substantial gaps in our understanding of the system. For example, as SFCDR loads decline, 

the main-stem CDR is an increasingly important source of 

particulate and dissolved cadmium and zinc, contributes one 

quarter of the total phosphorus load, and remains the main 

source of total and dissolved lead. Yet sampling in the mainstem CDR is limited to the few bridges in the 30-mile stretch. 

Isokinetic sampling from boats is possible but difficult during 

the high streamflow conditions that are critical to understanding this part of the system thus making bridge sampling highly 

preferable. Therefore, continuing to build on existing data 

records, including adding more years of data collection for 

the CDR at Rose Lake and continuing sampling at CDR near 

Cataldo and CDR near Harrison for the full suite of constituents, will help in establishing and monitoring long-term trends, 

particularly as remedial efforts shift towards this part of the 

CDR watershed.

This study focused on annual mean concentrations, 

annual total loads, and trends therein, but there are also 

WRTDS extensions available to explore trends in seasonal 

and mean monthly concentrations and loads (Choquette and 

others, 2019), which also could potentially help explain spatial 

and temporal loading dynamics for a variety of constituents. 

For example, considering data at a higher temporal resolution 

would likely yield insights into transport of particulate zinc 

and cadmium, which tend to be a minor fraction of these total 

metals but relatively more important during high streamflow 

events. Likewise, analysis of dissolved metals loading in 

the main-stem CDR during low streamflow might elucidate 

how loading dynamics associated with these constituents are 

changing over time. A thorough accounting of historical and 

current point sources and likely nonpoint contributions of 

phosphorus in the SFCDR between Kellogg and Pinehurst, 

paired with higher temporal resolution in loading data (that is, 

seasonal or monthly loads), would help in understanding the 

complex nutrient trends in this reach. Similarly, mechanisms 

of total phosphorus production and transport in the main-stem 

CDR are speculative and based on literature review; additional 

monitoring or higher resolution temporal analysis could be 

helpful for understanding total phosphorus transport in this 

part of the CDR watershed.

The limited streamflow analyses conducted here suggest 

that annual and seasonal streamflow maximums, medians, 

and minimums have not significantly changed in the past 30 

years. However, climate change is impacting streamflow in 

the region. For example, Clark (2010) examined multiple 

unregulated streams in Idaho and surrounding states and found 

significant shifts towards earlier spring runoff in the St. Joe 

River from 1967 to 2007. Looking at broader atmospheric 

climate signals across the Northwest, Abatzoglou and others 

(2014) found increased temperatures and increased spring and 

summer precipitation in northern Idaho. The most important 

loading events in the study area are the rare rain-on-snow 

events and the annual snowmelt runoff; shifts in precipitation and temperature patterns will affect streamflow patterns 

and likely affect these large loading events, but it is presently 

unclear how. A more extensive analysis of potential changes 

to snowmelt runoff magnitude, duration, and timing, and an 

examination of the frequency of the rarer rain-on-snow events 

would help elucidate potential impacts to loading in the study 

area and have potential ramifications for approaches to remedial actions moving forward.

Summary

Long-term surface water-quality monitoring data from 

the Coeur d’Alene River (CDR) and St. Joe and Spokane 

Rivers (collectively, “the study area”) were used to generate Weighted Regressions on Time, Discharge and Season 

(WRTDS) and WRTDS with Kalman filtering (WRTDS_K) 

models to estimate annual mean concentrations, annual total 

loads, flow-normalized annual mean concentrations, and 

flow-normalized annual total loads. Bootstrapped confidence 

intervals were constructed to determine the statistical likelihood of trends and the slope of trends in flow-normalized 

concentrations and loads over the period of record (which 
Acknowledgments 51

varied from 13 to 29 years), water years (WY) 1999–2009 and 

WYs 2009–2018. Constituents studied were total and dissolved cadmium, lead and zinc; total phosphorus and nitrogen; 

and total orthophosphate.

Throughout the study area at mining-affected sites, most 

metal loads and concentrations decreased with high statistical likelihoods over the period of record and WYs 2009–18. 

Specifically, total and dissolved zinc and cadmium concentrations and loads had “likely down” trends of about 25–75 

percent over the period of record and “likely down” trends 

of about 10–30 percent during WYs 2009–18. Total and 

dissolved lead concentrations and loads had “likely down” 

trends of about 20–85 percent over the period of record and 

had “likely down” or “somewhat likely down” trends of 

about 10–50 percent during WYs 2009–18. One exception 

to this was total lead load in CDR near Harrison, which had 

“somewhat likely up” trends for total lead over the period 

of record. Close temporal synchrony between statistically 

“likely down” trends in metal concentrations and loads and 

the onset of extensive remedial actions throughout the Bunker 

Hill Superfund Site indicate that remedial actions are improving water quality at mining-affected sites in the study area. 

Ambient water-quality criteria ratios for dissolved cadmium, 

lead, and zinc have consistently declined across miningaffected sites in the study area over the period of record, 

although concentrations remain above chronic aquatic criteria 

in most locations. Thus, although the effects of individual 

remedial actions on water-quality improvements cannot be 

discerned with this analysis, strong decreasing trends in metals 

concentrations and loads demonstrate that remedial actions 

over the last 30 years have improved water quality at miningaffected sites in the study area.

Analyses of incremental annual total load estimates 

illustrated spatial patterns in load sources in the study area 

and indicated some key locations for focusing future remedial 

efforts. Substantial loading of total lead in the South Fork 

Coeur d’Alene River (SFCDR) above Elizabeth Park may be 

related to tailings still located in the Osburn Flats area and 

represents an opportunity for additional remedial actions. The 

SFCDR remained the source of the majority of dissolved zinc 

and cadmium loads into Coeur d’Alene Lake, and the mainstem CDR remained the source of the majority of total and 

dissolved lead loads into Coeur d’Alene Lake. The main-stem 

CDR was also an important source of particulate cadmium and 

zinc, particularly during high streamflow years. These results 

were unsurprisingly but nonetheless important because remedial actions have not yet directly addressed widely dispersed 

particulate contaminants in the main-stem CDR system. The 

presence of these particulate contaminants, in conjunction with 

geochemical processes, also serve as a continuing source of 

dissolved lead, zinc, and cadmium in the main-stem CDR.

Trends in total phosphorus were variable both temporally and spatially in the study area during the period studied, but several broader patterns emerged. Temporally, total 

phosphorus loads and concentrations increased most during 

the 1990s, increased less during the 2000s, and decreased or 

remained the same during the 2010s. Spatially, the lack of 

consistent trends in the North Fork CDR, upper SFCDR, and 

St. Joe River, and inconsistencies between trends in upstream 

(SFCDR at Smelterville and SFCDR near Pinehurst) and 

downstream (CDR near Harrison) sites, strongly suggested 

that local processes and mechanisms were most important for 

driving changes. Analyses of incremental annual total loads 

indicated that the biggest phosphorus loads in the SFCDR 

and main-stem CDR occurred during high streamflow years, 

which points to the importance of phosphorus sources active 

during runoff conditions. In the SFCDR between Kellogg and 

Pinehurst, stormwater or other unaccounted surface runoffs 

may be important load sources, and these loads may have 

been more important in the 1990s and less so in the 2000s as 

remedial actions to limit surface erosion and revegetate landscapes began and took effect. In the CDR near Harrison, it is 

possible that near-record flooding in 1996 increased access to 

productive floodplains and lateral lakes in the main-stem CDR 

system, making total phosphorus more readily available for 

transport during subsequent runoff flows. However, mechanistic interpretations of the total phosphorus trends were fundamentally limited by the spatial and temporal sparseness of the 

underlying data and the relative paucity of technical information regarding phosphorus dynamics in the study area.

In summary, robust statistical analyses of long-term 

surface water-quality monitoring data in the Spokane River 

watershed are strong evidence of reduced metal concentrations and loads from the combined effects of remedial actions 

over the previous 30 years and yielded insights into the major 

source areas for metals and nutrients.

Acknowledgments

The analyses presented in this report would not have been 

possible without the dedication of numerous U.S. Geological Survey staff over many years and seasons, braving the 

elements to collect water-quality samples and streamflow 

measurements in every condition. The author appreciates the 

constructive reviews of an earlier manuscript draft by Chris 

Mebane and Bob Hirsch (U.S. Geological Survey), and Kim 

Prestbo and Chris Eckley (U.S. Environmental Protection 

Agency) which helped improve the final report.
52 Trends in Trace Metals and Nutrients in the Coeur d’Alene River Basin

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Appendix 1. 57

Appendix 1. Summary Graphs Showing Weighted Regressions on Time, 

Discharge and Season (WRTDS) and Weighted Regressions on Time, Discharge 

and Season with Kalman Filtering (WRTDS_K) Modeled Annual Concentrations 

and Loads

This appendix contains graphs showing annual mean concentrations and annual total loads and flow-normalized annual 

mean concentrations and annual total loads derived from the WRTDS and WRTDS_K models for each modeled site and constituent. The graphs can be accessed at https://doi.org/10.3133/sir20205096. Site locations can be seen in figure 1 in the main 

body of this report.
58 Trends in trace Metals and nutrients in the Coeur d’Alene River Basin

Appendix 2. Model Diagnostics

This appendix contains WRTDS model diagnostic graphs showing each modeled constituent for each modeled site. 

The graphs can be accessed at https://doi.org/10.3133/sir20205096. Site locations can be seen in figure 1 in the main body of 

this report.
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, Idaho Water Science Center 

U.S. Geological Survey 

230 Collins Rd 

Boise, Idaho 83702-4520 

https://www.usgs.gov/centers/id-water
Zinsser—Trends in Concentrations, Loads, and Sources of Trace Metals and Nutrients in the Spokane River Watershed, Northern Idaho, Water Years 1990–2018—SIR 2020–5096

ISSN 2331-1258 (online)

https://doi.org/10.3133/sir20205096