Climatic Fluctuations and Forecasting of Streamflow in the Lower Colorado River Basin1

Abstract:  Water‐resource managers need to forecast streamflow in the Lower Colorado River Basin to plan for water‐resource projects and to operate reservoirs for water supply. Statistical forecasts of streamflow based on historical records of streamflow can be useful, but statistical assumptions, such as stationarity of flows, need to be evaluated. This study evaluated the relation between climatic fluctuations and stationarity and developed regression equations to forecast streamflow by using climatic fluctuations as explanatory variables. Climatic fluctuations were represented by the Atlantic Multidecadal Oscillation (AMO), Pacific Decadal Oscillation (PDO), and Southern Oscillation Index (SOI). Historical streamflow within the 25‐ to 30‐year positive or negative phases of AMO or PDO was generally stationary. Monotonic trends in annual mean flows were tested at the 21 sites evaluated in this study; 76% of the sites had no significant trends within phases of AMO and 86% of the sites had no significant trends within phases of PDO. As climatic phases shifted in signs, however, many sites had nonstationary flows; 67% of the sites had significant changes in annual mean flow as AMO shifted in signs. The regression equations developed in this study to forecast streamflow incorporate these shifts in climate and streamflow, thus that source of nonstationarity is accounted for. The R² value of regression equations that forecast individual years of annual flow for the central part of the study area ranged from 0.28 to 0.49 and averaged 0.39. AMO was the most significant variable, and a combination of indices from both the Atlantic and Pacific Oceans explained much more variation in flows than only the Pacific Ocean indices. The average R² value for equations with PDO and SOI was 0.15.     

VARIATION IN THE RELATIONSHIP BETWEEN SNOWMELT RUNOFF IN OREGON AND ENSO AND PDO1

ABSTRACT: The value of using climate indices such as ENSO or PDO in water resources predictions is dependent on understanding the local relationship between these indices and streamflow over time. This study identifies long term seasonal and spatial variations in the strength of El Niño Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO) correlations with timing and magnitude of discharge in snowmelt streams in Oregon. ENSO is best correlated with variability in annual discharge, and PDO is best correlated with spring snowmelt timing and magnitude and timing of annual floods. Streams in the Cascades and Wallowa mountains show the strongest correlations, while the southernmost stream is not correlated with ENSO or PDO. ENSO correlations are weaker from 1920 to 1950 and vary significantly depending on whether Southern Oscillation Index (SOI) or Niño 3.4 is used. PDO correlations are strong from 1920 to 1950 and weak or insignificant other years. Although there are not consistent increasing or decreasing trends in annual discharge or spring snowmelt timing, there are significant increases in fractional winter runoff that are independent of precipitation, PDO, or ENSO and may indicate monotonic winter warming.     

Statistical Models to Predict and Assess Spatial and Temporal Low‐Flow Variability in New England Rivers and Streams

In the northern hemisphere, summer low flows are a key attribute defining both quantity and quality of aquatic habitat. I developed one set of models for New England streams/rivers predicting July/August median flows averaged across 1985–2015 as a function of weather, slope, % imperviousness, watershed storage, glacial geology, and soils. These models performed better than most United States Geological Survey models for summer flows developed at a statewide scale. I developed a second set of models predicting interannual differences in summer flows as a function of differences in air temperature, precipitation, the North Atlantic Oscillation (NAO) index, and lagged NAO. Use of difference equations eliminated the need for transformations and accounted for serial autocorrelations at lag 1. The models were used in sequence to estimate time series for monthly low flows and for two derived flow metrics (tenth percentile [Q10] and minimum 3‐in‐5 year average flows). The first metric is commonly used in assessing risk to low‐flow conditions over time, while the second has been correlated with increased probability of localized extinctions for brook trout. The flow metrics showed increasing trends across most of New England for 1985–2015. However, application of summer flow models with average and extreme climate projections to the Taunton River, Massachusetts, a sensitive watershed undergoing rapid development, projected that low‐flow metrics will decrease over the next 50 years.     

Relative Effects of Climate and Water Use on Base‐Flow Trends in the Lower Klamath Basin1

Abstract: Since the 1940s, snow water equivalent (SWE) has decreased throughout the Pacific Northwest, while water use has increased. Climate has been proposed as the primary cause of base‐flow decline in the Scott River, an important coho salmon rearing tributary in the Klamath Basin. We took a comparative‐basin approach to estimating the relative contributions of climatic and non‐climatic factors to this decline. We used permutation tests to compare discharge in 5 streams and 16 snow courses between “historic” (1942‐1976) and “modern” (1977‐2005) time periods, defined by cool and warm phases, respectively, of the Pacific Decadal Oscillation. April 1 SWE decreased significantly at most snow courses lower than 1,800 m in elevation and increased slightly at higher elevations. Correspondingly, base flow decreased significantly in the two streams with the lowest latitude‐adjusted elevation and increased slightly in two higher‐elevation streams. Base‐flow decline in the Scott River, the only study stream heavily utilized for irrigation, was larger than that in all other streams and larger than predicted by elevation. Based on comparison with a neighboring stream draining wilderness, we estimate that 39% of the observed 10 Mm³ decline in July 1‐October 22 discharge in the Scott River is explained by regional‐scale climatic factors. The remainder of the decline is attributable to local factors, which include an increase in irrigation withdrawal from 48 to 103 Mm³/year since the 1950s.     

CLIMATE VARIABILITY AND FLOOD FREQUENCY ESTIMATION FOR THE UPPER MISSISSIPPI AND LOWER MISSOURI RIVERS1

ABSTRACT: This paper considers the distribution of flood flows in the Upper Mississippi, Lower Missouri, and Illinois Rivers and their relationship to climatic indices. Global climate patterns including El Niño/Southern Oscillation, the Pacific Decadal Oscillation, and the North Atlantic Oscillation explained very little of the variations in flow peaks. However, large and statistically significant upward trends were found in many gauge records along the Upper Mississippi and Missouri Rivers: at Hermann on the Missouri River above the confluence with the Mississippi (p = 2 percent), at Hannibal on the Mississippi River (p < 0.1 percent), at Meredosia on the Illinois River (p = 0.7 percent), and at St. Louis on the Mississippi below the confluence of all three rivers (p = 1 percent). This challenges the traditional assumption that flood series are independent and identically distributed random variables and suggests that flood risk changes over time.     

COLUMBIA RIVER FLOW AND DROUGHT SINCE 17501

ABSTRACT: A network of 32 drought sensitive tree‐ring chronologies is used to reconstruct mean water year flow on the Columbia River at The Dalles, Oregon, since 1750. The reconstruction explains 30 percent of the variability in mean water year (October to September) flow, with a large portion of unexplained variance caused by underestimates of the most severe low flow events. Residual statistics from the tree‐ring reconstruction, as well as an identically specified instrumental reconstruction, exhibit positive trends over time. This finding suggests that the relationship between drought and streamflow has changed over time, supporting results from hydrologic models, which suggest that changes in land cover over the 20th Century have had measurable impacts on runoff production. Low pass filtering the flow record suggests that persistent low flows during the 1840s were probably the most severe of the past 250 years, but that flows during the 1930s were nearly as extreme. The period from 1950 to 1987 is anomalous in the context of this record for having no notable multiyear drought events. A comparison of the flow reconstruction to paleorecords of the Pacific Decadal Oscillation (PDO) and El Nino/Southern Oscillation (ENSO) support a strong 20th Century link between large scale circulation and streamflow, but suggests that this link is very weak prior to 1900.     

Application of Wavelet Coherence Method to Investigate Karst Spring Discharge Response to Climate Teleconnection Patterns

The impact of climate teleconnections on the regional hydrometeorology has been well studied, but very little effort has been made to relate climate teleconnections with groundwater flow variation. In this study, we used a wavelet coherence method to analyze monthly climate indices, precipitation, and spring discharge data, and investigated the relation between major teleconnection patterns (the Arctic Oscillation, North Atlantic Oscillation, Pacific Decadal Oscillation, El Niño‐Southern Oscillation, and Indian Ocean Dipole) and karst hydrological process in Niangziguan Springs Basin, China. The results indicate precipitation and spring discharges correlate well with climate indices at intra‐ and inter‐annual time scales. Further, the climate indices are mainly correlated with precipitation at shorter periodicities, but correlated with spring discharge at longer scales. The difference reflects the modulation of karst aquifers on precipitation‐spring discharge during the processes of precipitation infiltration into the ground, and subsequent transformation into spring discharge. When teleconnection signals are transmitted into spring discharge via precipitation infiltration and groundwater propagation, some high‐frequency climatic signals are likely to be filtered, attenuated, and delayed, thus only low‐frequency climatic signals are preserved in spring discharge.     

STREAMFLOW TRENDS IN WISCONSIN'S DRIFTLESS AREA1

ABSTRACT: Trends in streamflow characteristics were analyzed for streams in southwestern Wisconsin's Driftless Area by using data at selected gaging stations. The analyses indicate that annual low flows have increased significantly, whereas annual flood peaks have decreased. The same trends were not observed for forested areas of northern Wisconsin. Streamflow trends for other streams in southeastern Wisconsin draining predominantly agricultural land were similar to trends for Driftless Area streams for annual low flows. The causes for the trends are not well understood nor are the effects. Trends in annual precipitation do not explain the observed trends in streamflow. Other studies have found that erosion rates decreased significantly in the Driftless Area, and have attributed this reduction to a change of agricultural practices, which increase infiltration, decrease flood peaks, and increase low flows.     

Using Paleo Reconstructions to Improve Streamflow Forecast Lead Time in the Western United States

In water stressed regions, water managers are exploring new horizons that would help in long‐range streamflow forecasts. Oceanic‐atmospheric oscillations have been shown to influence streamflow variability. In this study, long‐lead time streamflow forecasts are made using a multiclass kernel‐based data‐driven support vector machine (SVM) model. The extended streamflow records based on tree ring reconstructions were used to provide a longer time series data. Reconstructed data were used from 1658 to 1952 and the instrumental record was used from 1953 to 2007. Reconstructions for oceanic‐atmospheric oscillations included the El Niño‐Southern Oscillation, Pacific Decadal Oscillation, Atlantic Multidecadal Oscillation, and North Atlantic Oscillation. Streamflow forecasts using all four oscillations were made with one‐year to five‐year lead times for 21 gages in the western United States. This is the first study that uses both instrumental and reconstructed data of oscillations in SVM model to improve streamflow forecast lead time. SVM model was able to provide “satisfactory” to “very good” forecasts with one‐ to five‐year lead time for the selected gages. The use of all the oscillation indices helped in achieving better predictability compared to using individual oscillations. The SVM modeling results are better when compared with multiple linear regression model forecasts. The findings are statistical in nature and are expected to be useful for long‐term water resources planning and management.     

Associations of Decadal to Multidecadal Sea‐Surface Temperature Variability with Upper Colorado River Flow1

Abstract: The relations of decadal to multidecadal (D2M) variability in global sea‐surface temperatures (SSTs) with D2M variability in the flow of the Upper Colorado River Basin (UCRB) are examined for the years 1906‐2003. Results indicate that D2M variability of SSTs in the North Atlantic, North Pacific, tropical Pacific, and Indian Oceans is associated with D2M variability of the UCRB. A principal components analysis (with varimax rotation) of detrended and 11‐year smoothed global SSTs indicates that the two leading rotated principal components (RPCs) explain 56% of the variability in the transformed SST data. The first RPC (RPC1) strongly reflects variability associated with the Atlantic Multidecadal Oscillation and the second RPC (RPC2) represents variability of the Pacific Decadal Oscillation, the tropical Pacific Ocean, and Indian Ocean SSTs. Results indicate that SSTs in the North Atlantic Ocean (RPC1) explain as much of the D2M variability in global SSTs as does the combination of Indian and Pacific Ocean variability (RPC2). These results suggest that SSTs in all of the oceans have some relation with flow of the UCRB, but the North Atlantic may have the strongest and most consistent association on D2M time scales. Hydroclimatic persistence on these time scales introduces significant nonstationarity in mean annual streamflow, with critical implications for UCRB water resource management.     

A NEW FLASHINESS INDEX: CHARACTERISTICS AND APPLICATIONS TO MIDWESTERN RIVERS AND STREAMS1

ABSTRACT: The term flashiness reflects the frequency and rapidity of short term changes in streamflow, especially during runoff events. Flashiness is an important component of a stream's hydrologic regime. A variety of land use and land management changes may lead to increased or decreased flashiness, often to the detriment of aquatic life. This paper presents a newly developed flashiness index, which is based on mean daily flows. The index is calculated by dividing the pathlength of flow oscillations for a time interval (i.e., the sum of the absolute values of day‐to‐day changes in mean daily flow) by total discharge during that time interval. This index has low interannual variability, relative to most flow regime indicators, and thus greater power to detect trends. Index values were calculated for 515 Midwestern streams for the 27‐year period from 1975 through 2001. Statistically significant increases were present in 22 percent of the streams, primarily in the eastern portion of the study area, while decreases were present in 9 percent, primarily in the western portion. Index values tend to decrease with increasing watershed area and with increasing unit area ground water inputs. Area compensated index values often shift at ecoregion boundaries. Potential index applications include evaluation of programs to restore more natural flow regimes.     

Observed Winter Warming of the Chesapeake Bay Estuary (1949–2002): Implications for Ecosystem Management

A large number of studies have documented 20th century climate variability and change at the global, hemispheric, and regional levels. However, understanding the implications of climate change for environmental management necessitates information at the level of the ecosystem. Historical monitoring data from the Chesapeake Bay estuary were used to identify temporal patterns of estuarine temperature anomalies in the surface (1 m) and subsurface (15 m) between 1949 and 2002. Data indicated a trend in surface and subsurface warming of +0.16°C and +0.21°C per decade, respectively, driven by warming during winter and spring. These trends suggest warming of the estuary since the mid-20th century of approximately 0.8–1.1°C. Estuarine temperatures correlated well with other independent data records for sea surface and surface air temperatures in the region and to a lesser extent, the northern hemisphere. Gross long-term temperature variability in the estuary was consistent with North Atlantic climate variability associated with the prolonged positive North Atlantic Oscillation/Arctic Oscillation and increased anthropogenic radiative forcing, although localized environmental drivers likely are important as well. A simple spatial analysis revealed strong seasonal latitudinal and longitudinal gradients in estuarine temperature as well as a north–south gradient in long-term temperature trends. Continued warming of the estuary will have important implications for ecosystem structure and function as well as attempts to manage existing challenges such as eutrophication and benthic hypoxia. However, such management efforts must be cognizant of the effects of various climate and nonclimate drivers of environmental variability and change operating over different spatial and temporal scales.Published online     

Stream Temperature Patterns over 35 Years in a Managed Forest of Western Washington

Stream temperature changes as a result of forest practices have been a concern in the Pacific Northwest for several decades. As a result of this concern, stream protection requirements for forest lands were first adopted in the early 1970s and have become progressively more stringent. While there have been multiple studies examining the effects of stream protection buffers on water temperature, there are few studies examining temperature patterns over long periods on intensively managed forests. Water temperature in the upper Deschutes River watershed, Washington has been monitored since 1975 and represents one of the longest studies of water quality on managed forests in the Pacific Northwest. This data record, collected from basins of varying sizes, has enabled us to examine the combined effects of hydro‐climatic patterns and forest management on stream temperature. Effects of harvest conducted prior to buffer regulations were clearly identifiable and most pronounced on smaller streams. We were not able to detect any response on larger channels to more recent timber harvest where riparian buffers were required. This analysis also emphasizes that it is critical to account for changing climate when examining long‐term temperature patterns. We found that in many cases the temperature improvements associated with more stringent buffer requirements implemented over the last 35 years in the Deschutes watershed have been offset by warming climatic conditions.     

IMPLICATIONS OF CLIMATIC VARIABILITY FOR REGULATORY LOW FLOWS IN THE SOUTH PLATTE RIVER BASIN,COLORADO1

ABSTRACT: The maximum concentration of a regulated substance that is allowed in a wastewater effluent usually is determined from the amount of dilution provided by the receiving water. Dilution flow is estimated from historical data by application of statistical criteria that define low flow conditions for regulatory purposes. Such use of historical data implies that the past is a good indicator of future conditions, at least for the duration of a discharge permit. Short records, however, introduce great uncertainty in the estimation of low flows because they are unlikely to capture events with recurrence frequencies of multiple years (e.g., ENSO events or droughts). We conducted an analysis of daily flows at several gages with long records in the South Platte River basin of Colorado. Low flows were calculated for successive time blocks of data (3‐, 5‐, 10‐, and 20‐years), and these were compared with low flows calculated for the entire period of record (> 70 years). In unregulated streams, time blocks of three or five years produce estimates of low flows that are highly variable and consistently greater than estimates derived from a longer period of record. Estimates of low flow from 10‐year blocks, although more stable, differ from the long term estimates by as much as a factor of two because of climate variation. In addition, the hydrographs of most streams in Colorado have been influenced by dams, diversions, or water transfers. These alterations to the natural flow regime shorten the record that is useful for analysis, but also tend to increase the calculated low flows. The presence of an upward trend in low flows caused by water use represents an unanticipated risk because it fails to incorporate societal response to severe drought conditions. Thus, climate variability poses a significant risk for water quality both directly, because it may not be represented adequately in the short periods of the hydrologic record that are typically used in permits, and indirectly, through its potential to cause altered use of water during time of scarcity.     

CLIMATE SCIENCE AND DROUGHT PLANNING: THE ARIZONA EXPERIENCE1

ABSTRACT: In response to recent severe drought conditions throughout the state, Arizona recently developed its first drought plan. The Governor's Drought Task Force focused on limiting the economic and social impacts of future droughts through enhanced adaptation and mitigation efforts. The plan was designed to maximize the use of new, scientific breakthroughs in climate monitoring and prediction and in vulnerability assessment. The long term objective of the monitoring system is to allow for evaluation of conditions in multiple sectors and at multiple scales. Stakeholder engagement and decision support are key objectives in reducing Arizona's vulnerability in light of the potential for severe, sustained drought. The drivers of drought conditions in Arizona include the El Nino‐Southern Oscillation, the Pacific Decadal Oscillation, and the Atlantic Multidecadal Oscillation.     

Hydrological classification of natural flow regimes to support environmental flow assessments in intensively regulated Mediterranean rivers, Segura River Basin (Spain)

Hydrological classification constitutes the first step of a new holistic framework for developing regional environmental flow criteria: the “Ecological Limits of Hydrologic Alteration (ELOHA)”. The aim of this study was to develop a classification for 390 stream sections of the Segura River Basin based on 73 hydrological indices that characterize their natural flow regimes. The hydrological indices were calculated with 25 years of natural monthly flows (1980/81–2005/06) derived from a rainfall-runoff model developed by the Spanish Ministry of Environment and Public Works. These indices included, at a monthly or annual basis, measures of duration of droughts and central tendency and dispersion of flow magnitude (average, low and high flow conditions). Principal Component Analysis (PCA) indicated high redundancy among most hydrological indices, as well as two gradients: flow magnitude for mainstream rivers and temporal variability for tributary streams. A classification with eight flow-regime classes was chosen as the most easily interpretable in the Segura River Basin, which was supported by ANOSIM analyses. These classes can be simplified in 4 broader groups, with different seasonal discharge pattern: large rivers, perennial stable streams, perennial seasonal streams and intermittent and ephemeral streams. They showed a high degree of spatial cohesion, following a gradient associated with climatic aridity from NW to SE, and were well defined in terms of the fundamental variables in Mediterranean streams: magnitude and temporal variability of flows. Therefore, this classification is a fundamental tool to support water management and planning in the Segura River Basin. Future research will allow us to study the flow alteration-ecological response relationship for each river type, and set the basis to design scientifically credible environmental flows following the ELOHA framework.     

ALTERNATIVE APPROACH TO THE FORMULATION OF BASIN HYDRAULIC GEOMETRY EQUATIONS1

ABSTRACT: Along a drainage network, there is a systematic variation of average flow parameters (width, depth, and velocity) at flows having the same flow duration. Hydraulic geometry equations mathematically express this interdependent relationship of stream-flow characteristics for a basin for annual flow durations varying from 10 to 90 percent. However, the equations proposed so far have had rather poor predictive performance for low flows. An independent investigation of the variation of discharge with drainage area and annual flow duration demonstrates a consistent relationship between these parameters. The relationship for the high to median-flow range differs, however, from that for the median— to low-flow range. The proposed equations provide a better predictive performance for low flows than previous formulations and a versatile means of estimating flow parameters for streams throughout a basin. The improved basin hydraulic geometry equations have a wide range of applications in areas such as stream habitat assessment, water quality modeling, channel design, and stream restoration projects.     

A Daily Time Series Analysis of StreamWater Phosphorus Concentrations Along an Urban to Forest Gradient

During a 1-year period, we sampled stream water total phosphorus (TP) concentrations daily and soluble reactive phosphorus (SRP) concentrations weekly in four Seattle area streams spanning a gradient of forested to urban-dominated land cover. The objective of this study was to develop time series models describing stream water phosphorus concentration dependence on seasonal variation in stream base flows, short-term flow fluctuations, antecedent flow conditions, and rainfall. Stream water SRP concentrations varied on average by ±18% or ±5.7 μg/L from one week to another, whereas TP varied ±48% or ±32.5 μg/L from one week to another. On average, SRP constituted about 47% of TP. Stream water SRP concentrations followed a simple sine-wave annual cycle with high concentrations during the low-flow summer period and low concentrations during the high-flow winter period in three of the four study sites. These trends are probably due to seasonal variation in the relative contributions of groundwater and subsurface flows to stream flow. In forested Issaquah Creek, SRP concentrations were relatively constant throughout the year except during the fall, when a major salmon spawning run occurred in the stream and SRP concentrations increased markedly. Stream water SRP concentrations were statistically unrelated to short-term flow fluctuations, antecedent flow conditions, or rainfall in each of the study streams. Stream water TP concentrations are highly variable and strongly influenced by short-term flow fluctuations. Each of the processes assessed had statistically significant correlations with TP concentrations, with seasonal base flow being the strongest, followed by antecedent flow conditions, short-term flow fluctuations, and rainfall. Times series models for each individual stream were able to predict ∼70% of the variability in the SRP annual cycle in three of the four streams (r² = 0.57–0.81), whereas individual TP models explained ∼50% of the annual cycle in all streams (r² = 0.39–0.59). Overall, time series models for SRP and TP dynamics explained 82% and 76% of the variability for these variables, respectively. Our results indicate that SRP, the most biologically available and therefore most important phosphorus fraction, has simpler and easier-to-predict seasonal and weekly dynamics.     

Long-Term Variability in Bioassessments: A Twenty-Year Study from Two Northern California Streams

Long-term variability of bioassessments has not been well evaluated. We analyzed a 20-year data set (1984–2003) from four sites in two northern California streams to examine the variability of bioassessment indices (two multivariate RIVPACS-type O/E scores and one multimetric index of biotic integrity, IBI), as well as eight metrics. All sites were sampled in spring; one site was also sampled in summer. Variability among years was high for most metrics (coefficients of variation, CVs ranging from 16% to 246% in spring) but lower for indices (CVs of 22–26% for the IBI and 21–32% for O/E scores in spring), which resulted in inconsistent assessments of biological condition. Variance components analysis showed that the time component explained variability in all metrics and indices, ranging from 5% to 35% of total variance explained. The site component was large (i.e., >40%) for some metrics (e.g., EPT richness), but nearly absent from others (e.g., Diptera richness). Seasonal analysis at one site showed that variability among seasons was small for some metrics or indices (e.g., Coleoptera richness), but large for others (e.g., EPT richness, O/E scores). Climatic variables did not show consistent trends across all metrics, although several were related to the El Ni?o Southern Oscillation Index at some sites. Bioassessments should incorporate temporal variability during index calibration or include climatic variability as predictive variables to improve accuracy and precision. In addition, these approaches may help managers anticipate alterations in reference streams caused by global climate change and high climatic variability.     

Pattern and Process in Northern Rocky Mountain Headwaters: Ecological Linkages in the Headwaters of the Crown of the Continent1

Abstract: The Crown of the Continent is one of the premiere ecosystems in North America containing Waterton‐Glacier International Peace Park, the Bob Marshall‐Great Bear‐Scapegoat Wilderness Complex in Montana, various Provincial Parks in British Columbia and Alberta, several national and state forest lands in the USA, and Crown Lands in Canada. The region is also the headwater source for three of the continent’s great rivers: Columbia, Missouri and Saskatchewan that flow to the Pacific, Atlantic and Arctic Oceans, respectively. Headwaters originate in high elevation alpine environs characterized by high snow accumulations in winter and rainstorms in summer. Most headwaters of the region contain high quality waters with few ions in solution and extremely low nutrient concentrations. Alpine streams have few species of aquatic organisms; however, they often possess rare species and have hydrogeomorphic features that make them vulnerable to climatic change. Subalpine and valley bottom streams of the Crown of the Continent Ecosystem (CCE) flow through well forested watersheds. Along the elevation gradient, the streams and rivers of the CCE flow through series of confining and nonconfining valleys resulting in distinct canyon and floodplain reaches. The alluvial floodplains are characterized by high species diversity and bioproduction maintained by the hydrologic linkages of habitats. The streams and rivers of the CCE have low nutrient concentrations, but may be significantly affected by wildfire, various resource extraction activities, such as logging or mining and exurban encroachment. Wildfire has been shown to increase nutrient loading in streams, both during a fire and then following the fire for as much as 5 years. Logging practices increase nutrient loading and the algal productivity of stream periphyton. Logging and associated roads are also known to increase sediment transport into Crown of the Continent streams directly affecting spawning success of native trout. The CCE is one of the fastest growing regions in the USA because of the many recreational amenities of the region. And, while the region has many remarkably pristine headwater streams and receiving rivers, there are many pending threats to water quality and quantity. One of the most urgent threats comes from the coal and gas fields in the northern part of the Crown of the Continent, where coal deposits are proposed for mountain‐top removal and open‐pit mining operations. This will have significant effects on the waters of the region, its native plants and animals and quality of life of the people.