Geology topics

Research about Klamath River

Source-linked reports with geographic coverage including Klamath River.

18 recordsLinked to original sources

USGS2026

Discharge magnitude drives interannual variation in distribution of the invertebrate host Manayunkia occidentalis of the salmon parasite Ceratonova shasta

Objective The objective of this study was to evaluate statistical evidence for relationships between flow event characteristics and annelid host distribution, an important and necessary step toward providing and justifying management actions. Declines in Klamath River salmon have been attributed to infection and disease that are caused by the myxozoan parasite Ceratonova shasta . Flow manipulation has been used to manage risk of C. shasta for juvenile salmonids in this system. One mechanism by which flow-related disturbance can reduce the risk of C. shasta infection for salmon is by reducing populations of the obligate invertebrate host Manayunkia occidentalis . We previously demonstrated that hydraulic conditions during peak discharge events drive the distribution of M. occidentalis and suggested that high-magnitude flow events would be effective for reducing the distribution of the annelid host. However, evidence of the effects of flow events on M. occidentalis was needed to support the use of flow management. Methods To address this knowledge gap, we leveraged a multiyear data set to estimate relationships between the distribution the annelid host and the characteristics of each discharge event. We measured the presence or absence of M. occidentalis at spatially georeferenced sampling locations, stratified across the range of hydraulic and substrate conditions in three reaches annually from 2012 to 2020. Results During the study period, the magnitude of peak discharge ranged from 52.4 to 314.3 m 3 /s. The inclusion of seven additional years’ data in the base model (hierarchical; annual-level covariate + previous “single year” model) resulted in parameter estimates that were similar to those that were derived for the previous (2016) model, supporting that substrate, depth, and velocity during peak discharge predicted annelid distribution. The magnitude model (base model + annual-level covariate for peak discharge) showed evidence of a strong negative association with annelid presence (95% of all Markov chain–Monte Carlo draws were negative). Every 101.9 m 3 /s increase in peak discharge was associated with an estimated 39% decrease in the odds of annelid presence. The estimated effect of magnitude on the probability of annelid presence was illustrated in the contrast between low- and high-magnitude peak discharge scenarios. For both scenarios, the effects of depth, velocity at peak discharge, and substrate, consistent with the previous model (2016), were evident, as was the further reduction in probability of annelid presence at the higher peak discharge. However, under the low-magnitude discharge scenario, M. occidentalis were predicted to be present on smaller less stable substrates and at a wider range of depths and velocities than they were under the high-magnitude discharge scenario. In contrast to the covariate for magnitude, the inclusion of a duration covariate did not show a strong relationship with annelid distribution, which we attributed to the lack of variation in this covariate during the study period. Conclusions This work provides quantitative evidence that high-magnitude peak discharge flow events lead to lower probabilities of annelid host presence. Lower probabilities of annelid hosts are indicative of a reduced distribution of the M. occidentalis host and in turn reduced risk of C. shasta for salmon.

California↗

USGS2025

Toward co-designed Earth System Models: Reflecting end-user priorities in local applications from a modeler's perspective

Earth System Models (ESM) are crucial for quantifying climate impacts across Earth's interconnected systems and supporting science-based adaptation and mitigation. However, not including end-users, especially decision-makers representing communities vulnerable to climate change, can limit model utility, increase epistemic risks, and lead to information misuse in decision-making. While the ESM community increasingly values broad community engagement, end-users may not initially perceive models as useful for local planning. Co-designing models with end-users fosters two-way learning: users better understand models and their outputs, while modelers gain insights into fine-scale local processes like monitoring practices and management priorities. Higher-level co-design can lead to more customized, priority-driven, and useful modeling products. Despite these benefits, modelers often struggle to initiate meaningful partnerships with local communities. Therefore, this paper explores model co-design from the perspective of modelers. This study presents two case studies where modelers and social scientists collaborated with Indigenous communities' decision-makers to reflect their priorities in model design and application. In the Arctic Rivers Project, high-resolution climate and hydrology data sets for Alaska were developed with guidance from an Indigenous Advisory Council, using optimized, coupled land-atmosphere models. In the Mid-Klamath Project, we partnered with the Karuk Tribe's Department of Natural Resources to assess climate change and prescribed burning impacts on terrestrial hydrology in the Klamath River Basin. Drawing from these studies, we introduce a four-level framework: (a) Co-design Configuration; (b) Model Tuning; (c) Incorporate Contextual Knowledge; (d) Co-develop New Model Functions. We aim to help researchers consider and compare co-design across diverse modeling projects systematically and coherently.

Alaska, California, Oregon↗

USGS2025

A molecular specimen bank for contemporary and future study captures landscape-scale biodiversity baselines before Klamath River dam removal

Global restoration and conservation of freshwater biodiversity are represented in practice by works such as the Klamath River Renewal Project (KRRP), the largest dam removal and river restoration in the United States, which has reconnected 640 river kilometers. With dam removals, many biological outcomes remain understudied due to a lack of pre-impact data and complex ecosystem recovery timeframes. To avoid this, we created the KRRP molecular library, an environmental specimen bank, for long-term curation of environmental nucleic acids collected from the restoration project. We used these initial samples, environmental DNA metabarcoding, and generalized linear mixed-effects models to evaluate patterns of pre-dam removal fish richness and diversity. Demonstrating the suitability to resolve biological differences, the baseline shows that tributary and mainstem streams had greater native fish diversity and 2.3–10.7 times greater native fish species richness than reservoirs. These and future sampling efforts should, at a minimum, allow tracking of fish community response to ecosystem restoration. Anticipating the acceleration of omics innovation, we preserved samples for long-term storage and identified requisite phases for sustained function and adaptation of the molecular library: securing a physical storage facility for genetic material, establishing a governance structure, and confirming support for archive management.

California, Oregon↗

USGS2023

Modeling the water-quality effects to the Klamath River from recirculation in drains and canals, Oregon and California, 2006–15

The potential recirculation of Klamath Strait Drain (hereafter called by its local name, “Klamath Straits Drain”) water into Ady Canal to reduce the drain discharge of high nutrient loads into the Klamath River was assessed by the U.S. Geological Survey for the Bureau of Reclamation. To study the feasibility of recirculation, this investigation evaluated three recirculation scenarios over a 10-year period from 2006 to 2015, as a series of 1-year model simulations. A combination of two existing hydrodynamic, water-temperature, and water-quality models (CE-QUAL-W2) were used, including (1) the Link-Keno reach of the Klamath River, using Klamath Straits Drain as a tributary and for calendar years 2006–11, and (2) the same Link-Keno model used for calendar years 2012–15 in combination with an independent Klamath Straits Drain model from 2012 to 2015. Model simulations using the water-quality models were configured for the base case conditions and three different sets of recirculation scenarios: the maximum year-round recirculation without limits (scenario 1), limited year-round recirculation fixed by the current pipe flow configuration (scenario 2), and limited seasonal recirculation (May–September) also fixed by the current pipe flow configuration (scenario 3). In the base case, estimates of annual average daily total nitrogen loads and daily total phosphorus loads exported to the Klamath River from the Klamath Straits Drain were as much as 3,060 and 457 pounds per day (lbs/day), respectively. Currently (2023), the Total Maximum Daily Loads allocations for the Klamath Straits Drain are 21 and 268 lbs/day for total phosphorus and total nitrogen, respectively, so these maximum estimates exceed the current Total Maximum Daily Loads by greater than an order of magnitude. With scenario 1, load reductions occurred year-round for all constituents evaluated (total nitrogen, total phosphorus, 5-day biochemical oxygen demand [BOD5], 5-day carbonaceous biochemical oxygen demand) for the Klamath Straits Drain discharging to the Klamath River. Scenario 2 also had large reductions in total nitrogen, total phosphorus, and BOD5 loads. Substantial reductions did occur for scenario 3 but were constrained to only the active recirculation period from May through September. Despite the restricted period, the average reductions in the annual average daily load for total phosphorus and total nitrogen were 32.1 percent and 26.5 percent, respectively. The Ady Canal diverts high nutrient loads from the Klamath River, so the loading tradeoffs to the Klamath River between no recirculation and the recirculation scenarios were calculated. On an annual basis, the overall net balance between the Klamath Straits Drain and Ady Canal resulted in more total nitrogen and total phosphorus load reductions to the Klamath River for the three recirculation scenarios than the base case, for most years. In contrast, the net balance for BOD5 loads was higher to the Klamath River for the three recirculation scenarios than the base case, for most years. With the recirculation scenarios, the optimal recirculation periods to benefit Ady Canal, Klamath River, and Klamath Straits Drain did not always coincide. Recirculation would be most effective at reducing loads toward the Klamath Straits Drain Total Maximum Daily Load allocations in the spring (March–May) of each year. However, recirculation during these months would also increase salinity in the Ady Canal. In summer, recirculation would reduce Klamath Straits Drain loads toward the Total Maximum Daily Load allocations, though recirculation could decrease Klamath River water quality mostly because of decreased withdrawals of Klamath River water by the Ady Canal. Scenario 3 avoided recirculation into Ady Canal in the early spring months when salinity concerns would be the highest, while still decreasing nutrient loads exported from the Klamath Straits Drain to the Klamath River in the summer months.

California, Oregon↗

USGS2021

Sediment mobility and river corridor assessment for a 140-kilometer segment of the main-stem Klamath River below Iron Gate Dam, California

This river corridor assessment documents sediment mobility and river response to flood disturbance along a 140-kilometer segment of the main-stem Klamath River below Iron Gate Dam, California. Field and remote sensing methods were used to assess fundamental indicators of active sediment transport and river response to a combination of natural runoff events and reservoir releases during the study period from 2005 to 2019. Discharge measurements at two gaged sites and bed-material samples at two ungaged sites provided direct and indirect evidence of mobile bed conditions, scour and fill, and surface flushing of fine sediment. Available remote-sensing datasets collected in 2005, 2009, 2010, and 2016 were used to determine sediment storage, flood inundation boundaries, and provide indirect evidence of flood-induced scour. These datasets validate channel-maintenance flows defined by Shea and others (2016). During the study period, flows greater than or equal to 6,030 cubic feet per second mobilized the substrate, caused localized scour, and flushed fine sediment from bar surfaces. Flows greater than or equal to 10,400 cubic feet per second stripped vegetation from bars and floodplains and produced deeper scour. Flood disturbance within the study reach is produced by the combined effect of natural flows and reservoir releases, which resulted in mobile bed conditions during the study period. Periodic scour and substrate disturbance are considered by the U.S. Fish and Wildlife Service to be integral for managing disease-induced mortality of juvenile and adult salmonids. Substrate conditions conducive to parasites that host infectious diseases, particularly Ceratonova shasta, occur periodically. Additional studies are required to determine whether disease prevalence can be mitigated by well-timed reservoir releases. Study results are useful for interpreting linkages among physical and biological processes and for evaluating the effectiveness of flow management targeted to improve river bed conditions for endangered salmonid populations.

California↗

USGS2019

Using the stream salmonid simulator (S3) to assess juvenile Chinook salmon (Oncorhynchus tshawytscha) production under historical and proposed action flows in the Klamath River, California

Executive Summary The production of Klamath River fall Chinook salmon ( Oncorhynchus tshawytscha ) in northern California and southern Oregon is thought to be limited by poor survival during freshwater juvenile life stages, in part a result of Ceratonova shasta —a highly infectious disease that can lead to high fish mortality. Higher flushing river flows are thought to affect the concentration of C. shasta spores, and in turn, juvenile salmon infection and mortality. The Stream Salmonid Simulator (S3) model was built to simulate the spatiotemporal dynamics of the growth, movement, and survival of juvenile salmon from spawning through migration to the Pacific Ocean in response to river flow, habitat availability, water temperature, and C. shasta spore concentrations. The S3 model has been calibrated to juvenile fall Chinook salmon abundances at a trap site within the Klamath River, and was specifically designed to provide objective predictions of juvenile salmon abundance and survival in relation to proposed flow management alternatives and resulting fish infection and mortality by C. shasta . Infection by C. shasta in the Klamath River is location specific, occurring in a “disease zone” with high spore concentrations. The spatial extent of this disease zone (from river kilometer 289.6 to 212.9) has been incorporated in the S3 model for the Klamath River, enabling the assessment of disease effects on fish at specific spatial locations such as the trap sampling sites, and for fish that were or were not exposed to the disease zone as they emigrate the Klamath River to the Pacific Ocean. Given the information gained from field observations on spore concentrations in relation to river flow, deliberations by resource managers resulted in the incorporation of springtime flushing flows in a Proposed Action (PA) scenario developed in part to lower spore concentrations within the disease zone. A Historical (HI) scenario based on the observed flows, temperatures, and spore concentrations from 2004 to 2016 was used to compare and contrast the potential benefits to juvenile salmon from PA flows in relation to the HI conditions.

California↗

USGS2019

Refining the Baseline Sediment Budget for the Klamath River, California

Four dams in the Klamath River Hydroelectric Project (KHP) in Oregon and California (Figure 1) are currently scheduled to be removed over a period of a few weeks or months, beginning in January 2021. The Klamath dam removal will be the largest in the world by almost all measures, and is an unprecedented opportunity to advance science of river responses to such events. The KHP contains approximately 10-12 million cubic meters of mostly fine sediment and model estimates suggest approximately 1/3-2/3 of this volume is expected to be eroded from reservoirs. Much of this sediment is expected to be eventually transported by the river to, or through, the Klamath River Estuary, a distance of more than 300 kilometers. To improve the success of restoration activities following dam removal, agencies must understand the baseline conditions for biological, chemical, and physical processes, prior to the removal. We expect large changes in water quality (turbidity, suspended sediment, dissolved oxygen, temperature, and algal toxins) and in fish habitat in the Hydroelectric Reach and the main-stem of the Klamath River to the ocean. For example, modeled sediment concentrations in the Klamath River during dam removal were estimated exceed 10,000 – 15,000 mg/L, depending on streamflows, location, and the dam removal process, and to remain > 100 – 1000 mg/L for months at a time. Final time to achieve background concentrations post dam removal may take over two years (Reclamation, 2011). Plans to assess many of these changes post-dam removal are still being formulated.

California, Oregon↗

USGS2018

Estimation of stream conditions in tributaries of the Klamath River, northern California

Because of their critical ecological role, stream temperature and discharge are requisite inputs for models of salmonid population dynamics. Coho Salmon inhabiting the Klamath Basin spend much of their freshwater life cycle inhabiting tributaries, but environmental data are often absent or only seasonally available at these locations. To address this information gap, we constructed daily averaged water temperature models that used simulated meteorological data to estimate daily tributary temperatures, and we used flow differentials recorded on the mainstem Klamath River to estimate daily tributary discharge. Observed temperature data were available for fourteen of the major salmon bearing tributaries, which enabled estimation of tributary-specific model parameters at those locations. Water temperature data from six mid-Klamath Basin tributaries were used to estimate a global set of parameters for predicting water temperatures in the remaining tributaries. The resulting parameter sets were used to simulate water temperatures for each of 75 tributaries from 1980-2015. Goodness-of-fit statistics computed from a cross-validation analysis demonstrated a high precision of the tributary-specific models in predicting temperature in unobserved years and of the global model in predicting temperatures in unobserved streams. Klamath River discharge has been monitored by four gages that broadly intersperse the 292 kilometers from the Iron Gate Dam to the Klamath River mouth. These gages defined the upstream and downstream margins of three reaches. Daily discharge of tributaries within a reach was estimated from 1980-2015 based on drainage-area proportionate allocations of the discharge differential between the upstream and downstream margin. Comparisons with measured discharge on Indian Creek, a moderate-sized tributary with naturally regulated flows, revealed that the estimates effectively approximated both the variability and magnitude of discharge.

California↗

USGS2015

Habitat suitability criteria via parametric distributions: estimation, model selection and uncertainty

Previous methods for constructing univariate habitat suitability criteria (HSC) curves have ranged from professional judgement to kernel-smoothed density functions or combinations thereof. We present a new method of generating HSC curves that applies probability density functions as the mathematical representation of the curves. Compared with previous approaches, benefits of our method include (1) estimation of probability density function parameters directly from raw data, (2) quantitative methods for selecting among several candidate probability density functions, and (3) concise methods for expressing estimation uncertainty in the HSC curves. We demonstrate our method with a thorough example using data collected on the depth of water used by juvenile Chinook salmon ( Oncorhynchus tschawytscha ) in the Klamath River of northern California and southern Oregon. All R code needed to implement our example is provided in the appendix. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

California, Oregon↗

USGS2014

Water-quality modeling of Klamath Straits Drain recirculation, a Klamath River wetland, and 2011 conditions for the Link River to Keno Dam reach of the Klamath River, Oregon

The upper Klamath River and adjacent Lost River are interconnected basins in south-central Oregon and northern California. Both basins have impaired water quality with Total Maximum Daily Loads (TMDLs) in progress or approved. In cooperation with the Bureau of Reclamation, the U.S. Geological Survey (USGS) and Watercourse Engineering, Inc., have conducted modeling and research to inform management of these basins for multiple purposes, including agriculture, endangered species protection, wildlife refuges, and adjacent and downstream water users. A water-quality and hydrodynamic model (CE-QUAL-W2) of the Link River to Keno Dam reach of the Klamath River for 2006–09 is one of the tools used in this work. The model can simulate stage, flow, water velocity, ice cover, water temperature, specific conductance, suspended sediment, nutrients, organic matter in bed sediment and the water column, three algal groups, three macrophyte groups, dissolved oxygen, and pH. This report documents two model scenarios and a test of the existing model applied to year 2011, which had exceptional water quality. The first scenario examined the water-quality effects of recirculating Klamath Straits Drain flows into the Ady Canal, to conserve water and to decrease flows from the Klamath Straits Drain to the Klamath River. The second scenario explicitly incorporated a 2.73×10 6 m 2 (675 acre) off-channel connected wetland into the CE-QUAL-W2 framework, with the wetland operating from May 1 through October 31. The wetland represented a managed treatment feature to decrease organic matter loads and process nutrients. Finally, the summer of 2011 showed substantially higher dissolved-oxygen concentrations in the Link-Keno reach than in other recent years, so the Link-Keno model (originally developed for 2006–09) was run with 2011 data as a test of model parameters and rates and to develop insights regarding the reasons for the improved water-quality conditions.

Oregon↗

USGS2013

Flow variation and substrate type affect dislodgement of the freshwater polychaete, Manayunkia speciosa

We quantified microscale flow forces and their ability to entrain the freshwater polychaete, Manayunkia speciosa, the intermediate host for 2 myxozoan parasites (Ceratomyxa shasta and Parvicapsula minibicornis) that cause substantial mortalities in salmonid fishes in the Pacific Northwest. In a laboratory flume, we measured the shear stress associated with 2 mean flow velocities and 3 substrates and quantified associated dislodgement of polychaetes, evaluated survivorship of dislodged polychaetes, and observed behavioral responses of the polychaetes in response to increased flow. We used a generalized linear mixed model to estimate the probability of polychaete dislodgement for treatment combinations of velocity (mean flow velocity = 55 cm/s with a shear velocity = 3 cm/s, mean flow velocity = 140 cm/s with a shear velocity = 5 cm/s) and substrate type (depositional sediments and analogs of rock faces and the filamentous alga, Cladophora). Few polychaetes were dislodged at shear velocities <3 cm/s on any substrate. Above this level of shear, probability of dislodgement was strongly affected by both substrate type and velocity. After accounting for substrate, odds of dislodgement were 8× greater at the higher flow. After accounting for velocity, probability of dislodgement was greatest from fine sediments, intermediate from rock faces, and negligible from Cladophora. Survivorship of dislodged polychaetes was high. Polychaetes exhibited a variety of behaviors for avoiding increases in flow, including extrusion of mucus, burrowing into sediments, and movement to lower-flow microhabitats. Our findings suggest that polychaete populations probably exhibit high resilience to flow-mediated disturbances.

California↗

USGS2012

Detection probability of an in-stream passive integrated transponder (PIT) tag detection system for juvenile salmonids in the Klamath River, northern California, 2011

A series of in-stream passive integrated transponder (PIT) detection antennas installed across the Klamath River in August 2010 were tested using tagged fish in the summer of 2011. Six pass-by antennas were constructed and anchored to the bottom of the Klamath River at a site between the Shasta and Scott Rivers. Two of the six antennas malfunctioned during the spring of 2011 and two pass-through antennas were installed near the opposite shoreline prior to system testing. The detection probability of the PIT tag detection system was evaluated using yearling coho salmon implanted with a PIT tag and a radio transmitter and then released into the Klamath River slightly downstream of Iron Gate Dam. Cormack-Jolly-Seber capture-recapture methods were used to estimate the detection probability of the PIT tag detection system based on detections of PIT tags there and detections of radio transmitters at radio-telemetry detection systems downstream. One of the 43 PIT- and radio-tagged fish released was detected by the PIT tag detection system and 23 were detected by the radio-telemetry detection systems. The estimated detection probability of the PIT tag detection system was 0.043 (standard error 0.042). Eight PIT-tagged fish from other studies also were detected. Detections at the PIT tag detection system were at the two pass-through antennas and the pass-by antenna adjacent to them. Above average river discharge likely was a factor in the low detection probability of the PIT tag detection system. High discharges dislodged two power cables leaving 12 meters of the river width unsampled for PIT detections and resulted in water depths greater than the read distance of the antennas, which allowed fish to pass over much of the system with little chance of being detected. Improvements in detection probability may be expected under river discharge conditions where water depth over the antennas is within maximum read distance of the antennas. Improvements also may be expected if additional arrays of antennas are used.

California↗

USGS2012

Effects of Iron Gate Dam discharge and other factors on the survival and migration of juvenile coho salmon in the lower Klamath River, northern California, 2006-09

Current management of the Klamath River includes prescribed minimum discharges intended partly to increase survival of juvenile coho salmon during their seaward migration in the spring. To determine if fish survival was related to river discharge, we estimated apparent survival and migration rates of yearling coho salmon in the Klamath River downstream of Iron Gate Dam. The primary goals were to determine if discharge at Iron Gate Dam affected coho salmon survival and if results from hatchery fish could be used as a surrogate for the limited supply of wild fish. Fish from hatchery and wild origins that had been surgically implanted with radio transmitters were released into the Klamath River slightly downstream of Iron Gate Dam at river kilometer 309. Tagged fish were used to estimate apparent survival between, and passage rates at, a series of detection sites as far downstream as river kilometer 33. Conclusions were based primarily on data from hatchery fish, because wild fish were only available in 2 of the 4 years of study. Based on an information-theoretic approach, apparent survival of hatchery and wild fish was similar, despite differences in passage rates and timing, and was lowest in the 54 kilometer (km) reach between release and the Scott River. Models representing the hypothesis that a short-term tagging- or handling-related mortality occurred following release were moderately supported by data from wild fish and weakly supported by data from hatchery fish. Estimates of apparent survival of hatchery fish through the 276 km study area ranged from 0.412 (standard error [SE] 0.048) to 0.648 (SE 0.070), depending on the year, and represented an average of 0.790 per 100 km traveled. Estimates of apparent survival of wild fish through the study area were 0.645 (SE 0.058) in 2006 and 0.630 (SE 0.059) in 2009 and were nearly identical to the results from hatchery fish released on the same dates. The data and models examined supported positive effects of water temperature, river discharge, and fish weight as factors affecting apparent survival in the Klamath River upstream of the confluence with the Shasta River, but few of the variables examined were supported as factors affecting survival farther downstream. The effect of water temperature on apparent survival upstream of the Shasta River was greater than Iron Gate Dam discharge, which was greater than fish weight. The estimated effect on apparent survival between release and the Shasta River with each 1degree Celsius increase in water temperature was 1.4 times the effect of a 100 cubic feet per second increase in Iron Gate Dam discharge and 2.5 times the effect of a 1 gram increase in fish weight, and the effects of discharge and weight diminished at higher water temperatures up to the 17.91 degrees Celsius maximum present in the data examined. The rate of passage at the detection site near the confluence with the Shasta River was primarily affected by date of release, and water temperature was the only factor supported at the site near the confluence with the Scott River. Passage rates at sites downstream of the Scott River were affected by several of the variables examined, but the estimated effects were small and often imprecise. Results from this study indicate that discharge at Iron Gate Dam has a positive effect on apparent survival of yearling coho salmon in the Klamath River upstream of the Shasta River, but the effects are smaller than those of water temperature and are mediated by it. The results also support the use of hatchery fish as surrogates for wild fish in studies of apparent survival, but the available evidence suggests that study fish should be released well upstream of the area of interest, due to short-term differences in survival and migration behavior of hatchery and wild fish after release.

California↗

USGS2010

Controls on biochemical oxygen demand in the upper Klamath River, Oregon

A series of 30-day biochemical oxygen demand (BOD) experiments were conducted on water column samples from a reach of the upper Klamath River that experiences hypoxia and anoxia in summer. Samples were incubated with added nitrification inhibitor to measure carbonaceous BOD (CBOD), untreated to measure total BOD, which included demand from nitrogenous BOD (NBOD), and coarse-filtered to examine the effect of removing large particulate matter. All BOD data were fit well with a two-group model, so named because it considered contributions from both labile and refractory pools of carbon: BOD t = a 1 (1 − e − a 0 t ) + a 2 t . Site-average labile first-order decay rates a 0 ranged from 0.15 to 0.22/day for CBOD and 0.11 to 0.29/day for BOD. Site-average values of refractory zero-order decay rates a 2 ranged from 0.13 to 0.25 mg/L/day for CBOD and 0.01 to 0.45 mg/L/day for BOD; the zero-order CBOD decay rate increased from early- to mid-summer. Values of ultimate CBOD for the labile component a 1 ranged from 5.5 to 28.8 mg/L for CBOD, and 7.6 to 30.8 mg/L for BOD. Two upstream sites had higher CBOD compared to those downstream. Maximum measured total BOD 5 and BOD 30 during the study were 26.5 and 55.4 mg/L; minimums were 4.2 and 13.6 mg/L. For most samples, the oxygen demand from the three components considered here were: labile CBOD > NBOD > refractory CBOD, though the relative importance of refractory CBOD to oxygen demand increased over time. Coarse-filtering reduced CBOD for samples with high particulate carbon and high biovolumes of Aphanizomenon flos-aquae . There was a strong positive correlation between BOD, CBOD, and the labile component of CBOD to particulate C and N, with weaker positive correlation to field pH, field dissolved oxygen, and total N. The refractory component of CBOD was not correlated to particulate matter, instead showing weak but statistically significant correlation to dissolved organic carbon, UV absorbance at 254 nm, and total N. Particulate organic matter, especially the alga A. flos-aquae , is an important component of oxygen demand in this reach of the Klamath River, though refractory dissolved organic matter would continue to exert an oxygen demand over longer time periods and as water travels downstream.

Oregon↗

USGS2010

Application of the Systems Impact Assessment Model (SIAM) to fishery resource issues in the Klamath River, California

At the request of two offices of the U.S. Fish and Wildlife Service (FWS) located in Yreka and Arcata, Calif., we applied the Systems Impact Assessment Model (SIAM) to analyze a variety of water management concerns associated with the Federal Energy Regulatory Commission (FERC) relicensing of the Klamath hydropower projects or with ongoing management of anadromous fish stocks in the mainstem Klamath River, Oregon and California. Requested SIAM analyses include predicted effects of reservoir withdrawal elevations, use of full active storage in Copco and Iron Gate Reservoirs to augment spring flows, and predicted spawning and juvenile outmigration timing of fall Chinook salmon. In an effort to further refine the analysis of spring flow effects on predicted fall Chinook production, additional SIAM analyses were performed for predicted response to spring flow release variability from Iron Gate Dam, high and low pulse flow releases, the predicted effects of operational constraints for both Upper Klamath Lake water surface elevations, and projected flow releases specified in the Klamath Project 2006 Operations Plan (April 10, 2006). Results of SIAM simulations to determine flow and water temperature relationships indicate that up to 4 degrees C of thermal variability can be attributed to flow variations, but the effect is seasonal. Much more of thermal variability can be attributed to air temperature variations, up to 6 degrees C. Reservoirs affect the annual thermal signature by delaying spring warming by about 3 weeks and fall cooling by about 2 weeks. Multi-level release outlets on Iron Gate Dam would have limited utility; however, if releases are small (700 cfs) and a near-surface and bottom-level outlet could be blended, then water temperature may be reduced by 2-4 degrees C for a 4-week period during September. Using the full active storage in Copco and Iron Gate Reservoir, although feasible, had undesirable ramifications such as earlier spring warming, loss of hydropower production, and inability to re-fill the reservoirs without causing shortages elsewhere in the system. Altering spawning and outmigration timing may be important management objectives for the salmon fishery, but difficult to implement. SIAM predicted benefits that might occur if water temperature was cooler in fall and spring emergence was advanced; however, model simulations were based on purely arbitrary thermal reductions. Spring flow variability did indicate that juvenile fall Chinook rearing habitat was the major biological 'bottleneck' for year class success. Rearing habitat is maximal in a range between 4,500 and 5,500 cfs below Iron Gate Dam. These flow levels are not typically provided by Klamath River system operations, except in very wet years. The incremental spring flow analysis provided insight into when and how long a pulse flow should occur to provide predicted fall Chinook salmon production increases. In general, March 15th - April 30th of any year was the period for pulse flows and 4000 cfs was the target flow release that provided near-optimal juvenile rearing habitat. Again, competition for water resources in the Klamath River Basin may make implementation of pulsed flows difficult.

California, Oregon↗

USGS2009

Development and validation of a quantitative PCR to detect Parvicapsula minibicornis and comparison to histologically ranked infection of juvenile Chinook salmon, Oncorhynchus tshawytscha (Walbaum), from the Klamath River, USA

Parvicapsula minibicornis is a myxosporean parasite that is associated with disease in Pacific salmon during their freshwater life history phase. This study reports the development of a quantitative (real-time) polymerase chain reaction (QPCR) to detect P. minibicornis DNA. The QPCR assay targets the 18S ribosomal subunit gene. A plasmid DNA control was developed to calibrate cycle threshold (C T ) score to plasmid molecular equivalent (PME) units, a measure of gene copy number. Assay validation revealed that the QPCR was sensitive and able to detect 50 ag of plasmid DNA, which was equivalent to 12.5 PME. The QPCR assay could detect single P. minibicornis actinospores well above assay sensitivity, indicating a single spore contains at least 100 times the 18S DNA copies required for detection. The QPCR assay was repeatable and highly specific; no detectable amplification was observed using DNA from related myxozoan parasites. The method was validated using kidney tissues from 218 juvenile Chinook salmon sampled during the emigration period of March to July 2005 from the Klamath River. The QPCR assay was compared with histological examination. The QPCR assay detected P. minibicornis infection in 88.1% of the fish sampled, while histological examination detected infection in 71.1% of the fish sampled. Good concordance was found between the methods as 80% of the samples were in agreement. The majority of the disconcordant fish were positive by QPCR, with low levels of P. minibicornis DNA, but negative by histology. The majority of the fish rated histologically as having subclinical or clinical infections had high QPCR levels. The results of this study demonstrate that QPCR is a sensitive quantitative tool for evaluating P. minibicornis infection in fish health monitoring studies. ?? 2008 Blackwell Publishing Ltd.

California, Oregon↗

USGS2006

Assessment of factors limiting Klamath River fall Chinook salmon production potential using historical flows and temperatures

We parameterized and applied a deterministic salmon production model to infer the degree to which river flows and temperatures may limit freshwater production potential of the Klamath River in California. Specific parameter requirements, data sources, and significant assumptions are discussed in detail. Model simulations covered a wide variety of historical hydrologic and meteorologic conditions for 40+ years of environmental data. The model was calibrated only qualitatively, appearing to perform well in predicted outmigrant timing, but overestimating growth. Egg-to-outmigrant survival was near that reported for other rivers north of the Klamath River. Predicted production potential appeared to be determined by multiple causes involving both regularly occurring habitat-related constraints and irregularly occurring exposure to high water temperatures. Simulated production was greatest in years of intermediate water availability and was constrained in both dry and wet years, but for different reasons. Reducing mortality associated with limitations to juvenile habitat, if possible, would be expected to have the highest payoff in increasing production. Water temperature was important in determining predicted production in some years but overall was not predicted to be as important as physical microhabitat. No single mortality cause acted as a true “bottleneck” on production. Model uncertainty is addressed through a sensitivity analysis. Predicted habitat area may be a large source of model uncertainty and sensitivity, but collectively, model parameters associated with timing of events (for example spawning, fry emergence, and emigration) or related triggers control much of the model sensitivity. Though model uncertainty remains, one can begin to explore potential alternatives to reduce production limitations. Specific recommendations are made regarding future study and reducing uncertainty.

California, Oregon↗

USGS2001

Modeling Klamath River system operations for quantity and quality

Alternative water management scenarios for a portion of the mainstem Klamath River from Keno, Oregon, to Seiad Valley, California, were evaluated using computer models of water quantity (MODSIM) and quality (HEC-5Q). These models were used to explore the potential for changing system operations to improve summer/fall water quality conditions to benefit declining anadromous fish populations such as steelhead, coho, and fall chinook salmon. By comparing and contrasting several model simulation results, some operational strategies that could improve water quality were determined. Most of the alternatives evaluated decreased water temperature less than 2°C. For some alternatives, dissolved oxygen could be changed as much as 5 mg/L, but was often reduced, rather than increased (or improved). Resource managers need to be made aware that implementation of any strategy to enhance water quality conditions in the Klamath River could produce desirable beneficial results that are both spatially and temporally limited. In addition, undesirable water quality conditions, i.e., higher water temperature or lower dissolved oxygen concentration at other upstream or downstream locations, may also result.

California, Oregon↗