Regulated flushing in a gravel-bed river for channel habitat maintenance: A Trinity River fisheries case study

The operation of Trinity and Lewiston Dams on the Trinity River in northern California in the United States, combined with severe watershed erosion, has jeopardized the existence of prime salmonid fisheries. Extreme streamflow depletion and stream sedimentation below Lewiston have resulted in heavy accumulation of coarse sediment on riffle gravel and filling of streambed pools, causing the destruction of spawning, nursery, and overwintering habitat for prized chinook salmon (Salmo gairdnerii) and steelhead trout (Oncorhynchus tschawytscha). Proposals to restore and maintain the degraded habitat include controlled one-time remedial peak flows or annual maintenance peak flows designed to flush the spawning gravel and scour the banks, deltas, and pools. The criteria for effective channel restoration or maintenance by streambed flushing and scouring are examined here, as well as the mechanics involved.The liabilities of releasing mammoth scouring-flushing flows approximating the magnitude that preceded reservoir construction make this option unviable. The resulting damage to fish habitat established under the postproject streamflow regime, as well as damage to human settlements in the floodplain, would be unacceptable, as would the opportunity costs to hydroelectric and irrigation water users. The technical feasibility of annual maintenance flushing flows depends upon associated mechanical and structural measures, particularly instream maintenance dredging of deep pools and construction of a sediment control dam on a tributary where watershed erosion is extreme. The cost effectiveness of a sediment dam with a limited useful economic life, combined with perpetual maintenance dredging, is questionable.     

A MATHEMATICAL MODEL OF SALMONID SPAWNING HABITAT1

ABSTRACT: A simulation model [Salmonid Spawning Analysis Model (SSAM)] was developed as a management tool to evaluate the relative impacts of stream sediment load and water temperature on salmonid egg survival. The model is useful for estimating acceptable sediment loads to spawning habitat that may result from upland development, such as logging and agriculture. Software in common use in the USA were adapted for use in gravel bedded rivers and linked to simulate water temperature (the USFWS Instream Water Temperature, SNTEMP model) and water and sediment routing (the USAE Scour and Deposition in Rivers and Reservoirs, HEC-6 model, version 3.2). These models drive the redd (spawning nest) model (the USDA-ABS Sediment Intrusion Dissolved Oxygen SIDO model) which simulates sediment intrusion and dissolved oxygen concentration in the redd environment. The SSAM model predictions of dissolved oxygen and water temperature compared favorably with field data from artificial redds containing hatchery chinook salmon eggs.     

REACH SCALE HYDRAULIC ASSESSMENT OF INSTREAM SALMONID HABITAT RESTORATION1

ABSTRACT: This study investigates the use of a two‐dimensional hydrodynamic model (River2D) for an assessment of the effects of instream large woody debris and rock groyne habitat structures. The bathymetry of a study reach (a side channel of the Chilliwack River located in southwestern British Columbia) was surveyed after the installation of 11 instream restoration structures. A digital elevation model was developed and used with a hydrodynamic model to predict local velocity, depth, scour, and habitat characteristics. The channel was resurveyed after the fall high‐flow season during which a bankfull event occurred. Pre‐flood and post‐flood bathymetry pool distributions were compared. Measured scour was compared to predicted shear and pre‐flood and post‐flood fish habitat indices for coho salmon (Oncorhynchus kisutch) and steelhead trout (O. mykiss) were compared. Two‐dimensional flow model velocity and depth predictions compare favorably to measured field values with mean standard errors of 24 percent and 6 percent, respectively, while areas of predicted high shear coincide with the newly formed pool locations. At high flows, the fish habitat index used (weighted usable area) increased by 150 percent to 210 percent. The application of the hydrodynamic model indicated a net habitat benefit from the restoration activities and provides a means of assessing and optimizing planned works.     

A Review of Habitat Connectivity Research for Pacific Salmon in Marine,Estuary, and Freshwater Environments

Long‐term conservation planning for diadromous fishes would benefit from a better understanding of both the role of connectivity among environments and habitat variability in the expression of life‐history diversity. Most of the scientific knowledge on habitat fragmentation and connectivity has been developed in terrestrial systems in the discipline of landscape ecology. Research on habitat connectivity in aquatic systems (e.g., salmonid research that spans the spectrum of habitats from freshwater to the sea) is uncommon and largely focused on barriers to fish passage. Here, we present a review of the literature characterizing current research patterns on habitat connectivity within and among environments for Pacific salmon. We found this topic is still incipient: the literature is dominated by studies of freshwaters, with few articles focusing on habitat needs in estuary and marine systems. Pan‐environment studies are rare, pointing to a gap in our understanding of complex habitat relationships that might be significant in the development of long‐term conservation and restoration plans for Pacific salmon, particularly in light of the potential impact of climate change.     

Modeling the Relations Between Flow Regime Components,Species Traits,and Spawning Success of Fishes in Warmwater Streams

Modifications to stream hydrologic regimes can have a profound influence on the dynamics of their fish populations. Using hierarchical linear models, we examined the relations between flow regime and young-of-year fish density using fish sampling and discharge data from three different warmwater streams in Illinois, Alabama, and Georgia. We used an information theoretic approach to evaluate the relative support for models describing hypothesized influences of five flow regime components representing: short-term high and low flows; short-term flow stability; and long-term mean flows and flow stability on fish reproductive success during fish spawning and rearing periods. We also evaluated the influence of ten fish species traits on fish reproductive success. Species traits included spawning duration, reproductive strategy, egg incubation rate, swimming locomotion morphology, general habitat preference, and food habits. Model selection results indicated that young-of-year fish density was positively related to short-term high flows during the spawning period and negatively related to flow variability during the rearing period. However, the effect of the flow regime components varied substantially among species, but was related to species traits. The effect of short-term high flows on the reproductive success was lower for species that broadcast their eggs during spawning. Species with cruiser swimming locomotion morphologies (e.g., Micropterus) also were more vulnerable to variable flows during the rearing period. Our models provide insight into the conditions and timing of flows that influence the reproductive success of warmwater stream fishes and may guide decisions related to stream regulation and management.     

Using Instream Water Temperature Forecasts for Fisheries Management: An Application in the Pacific Northwest1

Huang, Biao, Christian Langpap, and Richard M. Adams, 2011. Using Instream Water Temperature Forecasts for Fisheries Management: An Application in the Pacific Northwest. Journal of the American Water Resources Association (JAWRA) 47(4):861‐876. DOI: 10.1111/j.1752‐1688.2011.00562.x Abstract: Water temperature is an important factor affecting aquatic life within the stream environment. Cold water species, such as salmonids, are particularly susceptible to elevated water temperatures. This paper examines the potential usefulness of short‐term (7 to 10 days) water temperature forecasts for salmonid management. Forecasts may be valuable if they allow the water resource manager to make better water allocation decisions. This study considers two applications: water releases from Lewiston Dam for management of adult Chinook salmon (Oncorhynchus tshawytscha) in the Klamath River and leasing water from agriculture for management of steelhead trout (Oncorhynchus mykiss) in the John Day River. We incorporate biophysical models and water temperature distribution data into a Bayesian framework to simulate changes in fish populations and the corresponding opportunity cost of water under different levels of temperature forecast reliability. Simulation results indicate that use of the forecasts results in increased fish production and that marginal costs decline as forecast reliability increases, suggesting that provision and use of such stream temperature forecasts would have potential value to society.     

Flow‐Biology Relationships Based on Fish Habitat Guilds in North Carolina

The health of freshwater biota is dependent on streamflow, yet identification of the flow regimes required to maintain ecological integrity remains challenging to states in the United States seeking to establish ecological flows. We tested the relationship between decreases in streamflow and Shannon‐Weaver diversity index of fish species for four flow‐based habitat guilds: riffle, riffle‐run, pool‐run, and pool in North Carolina. We found species that prefer shallow habitats, such as riffles and riffle‐runs were the most sensitive to decreases in streamflow; whereas no significant relationships were found for pool or pool‐run species. The sensitivity to decreases in streamflow was greatest during summer and fall, when streams are naturally lower. When all fish habitat guilds were included in the assessment of flow‐biology relationships, there were no significant relationships to decreases in streamflow. As the sensitivity of fish to reductions in streamflow is not constant across habitat guilds, combining all fish species together for flow‐biology analyses may greatly underestimate the response of fish species to decreases in flow and should be acknowledged when establishing ecological flows.     

Elements of a cost-benefit analysis for improving salmonid spawning habitat in the River Wye

Contingent valuation methods were used to derive an economic value for salmonid spawning habitat restoration. Anglers' willingness to pay for such restoration and farmers' willingness to accept compensation for lost productivity due to the restoration were investigated using questionnaire and face-to-face surveys, respectively. These elements were combined with the Wye Habitat Improvement Project (WHIP) budget into a cost-benefit analysis (CBA) based upon direct use values only. The CBA assumed that the WHIP will improve salmonid stock. Different levels of investment were considered and the CBA gave a positive net present value indicating an economically viable project and benefit-to-cost ratios greater than one for minor projects. However, the number of anglers using the Wye would need to double or triple in order to justify the full WHIP budget. Management of an environmental resource must consider users' and stakeholders' needs and opinions. It was found that anglers on the Wye value habitat/scenery in its own right and that this played an important part in the activity. Farmers' agreement regarding involvement in such projects was more likely to be determined by their political and ethical views than receiving an economic compensation.     

The need for constructing endangered fish habitats that conform to climate-driven flow changes in a western U.S. river

Warmwater fish habitat in the San Juan River of the southwestern United States has been reduced by over 30% as a result of water depletion, reservoir inundation, and cold-water dam releases combined with drought-related changes in hydrology. This reduction and a suite of other factors have contributed to declines in native fish populations including the federally endangered Colorado Pikeminnow (Ptychocheilus lucius) and Razorback Sucker (Xyrauchen texanus). Conservation efforts for these species include determining flow needs; protecting, managing, and augmenting habitats; and stocking hatchery fish. But the young of stocked fish have low survival due largely to a paucity of nursery habitat not being reformed and maintained under current conditions. Flow recommendations for Navajo Dam releases designed to mimic the river's natural hydrograph have not been met due to water shortages, and the desired outcomes of increased channel complexity and enhanced fish habitat have not been observed. Forecasted hydrology that includes ongoing drought shows that achieving the flow targets through further dam reoperations is unlikely. Mechanical construction of early life-stage habitats is a highly recommended complement to flow management for offsetting the effects of flow reduction and habitat loss. Habitats with features that are effective and resilient under a range of flows are important in counterbalancing the effects of climate change.     

Predicting the Thermal Effects of Dam Removal on the Klamath River

The Klamath River once supported large runs of anadromous salmonids. Water temperature associated with multiple mainstem hydropower facilities might be one of many factors responsible for depressing Klamath salmon stocks. We combined a water quantity model and a water quality model to predict how removing the series of dams below Upper Klamath Lake might affect water temperatures, and ultimately fish survival, in the spawning and rearing portions of the mainstem Klamath. We calibrated the water quantity and quality models and applied them for the hydrometeorological conditions during a 40-year postdam period. Then, we hypothetically removed the dams and their impoundments from the models and reestimated the rivers water temperatures. The principal thermal effect of dam and reservoir removal would be to restore the timing (phase) of the rivers seasonal thermal signature by shifting it approximately 18 days earlier in the year, resulting in river temperatures that more rapidly track ambient air temperatures. Such a shift would likely cool thermal habitat conditions for adult fall chinook (Oncorhynchus tshawytscha) during upstream migration and benefit mainstem spawning. By contrast, spring and early summer temperatures could be warmer without dams, potentially harming chinook rearing and outmigration in the mainstem. Dam removal might affect the rivers thermal regime during certain conditions for over 200 km of the mainstem.     

A Simple Model that Identifies Potential Effects of Sea-Level Rise on Estuarine and Estuary-Ecotone Habitat Locations for Salmonids in Oregon, USA

Diadromous aquatic species that cross a diverse range of habitats (including marine, estuarine, and freshwater) face different effects of climate change in each environment. One such group of species is the anadromous Pacific salmon (Oncorhynchus spp.). Studies of the potential effects of climate change on salmonids have focused on both marine and freshwater environments. Access to a variety of estuarine habitat has been shown to enhance juvenile life-history diversity, thereby contributing to the resilience of many salmonid species. Our study is focused on the effect of sea-level rise on the availability, complexity, and distribution of estuarine, and low-freshwater habitat for Chinook salmon (Oncorhynchus tshawytscha), steelhead (anadromous O. mykiss), and coho salmon (O. kisutch) along the Oregon Coast under future climate change scenarios. Using LiDAR, we modeled the geomorphologies of five Oregon estuaries and estimated a contour associated with the current mean high tide. Contour intervals at 1- and 2-m increments above the current mean high tide were generated, and changes in the estuary morphology were assessed. Because our analysis relied on digital data, we compared three types of digital data in one estuary to assess the utility of different data sets in predicting the changes in estuary shape. For each salmonid species, changes in the amount and complexity of estuarine edge habitats varied by estuary. The simple modeling approach we applied can also be used to identify areas that may be most amenable to pre-emptive restoration actions to mitigate or enhance salmonid habitat under future climatic conditions.     

Toward efficient riparian restoration: integrating economic, physical, and biological models

This paper integrates economic, biological, and physical models to explore the efficient combination and spatial allocation of conservation efforts to protect water quality and increase salmonid populations in the Grande Ronde basin, Oregon. We focus on the effects of shade on water temperatures and the subsequent impacts on endangered juvenile salmonid populations. The integrated modeling system consists of a physical model that links riparian conditions and hydrological characteristics to water temperature; a biological model that links water temperature and riparian conditions to salmonid abundance, and an economic model that incorporates both physical and biological models to estimate minimum cost allocations of conservation efforts. Our findings indicate that conservation alternatives such as passive and active riparian restoration, the width of riparian restoration zones, and the types of vegetation used in restoration activities should be selected based on the spatial distribution of riparian characteristics in the basin. The relative effectiveness of passive and active restoration plays an important role in determining the efficient allocations of conservation efforts. The time frame considered in the restoration efforts and the magnitude of desired temperature reductions also affect the efficient combinations of restoration activities. If the objective of conservation efforts is to maximize fish populations, then fishery benefits should be directly targeted. Targeting other criterion such as water temperatures would result in different allocations of conservation efforts, and therefore are not generally efficient.     

Recovery of temperate-stream fish communities from disturbance: A review of case studies and synthesis of theory

To evaluate the relative effect of autecologic factors, site-specific factors, disturbance characteristics, and community structure on the recovery of temperate-stream fish communities, we reviewed case histories for 49 sites and recorded data on 411 recovery end points. Most data were derived from studies of low-gradient third- or fourth-order temperate streams located in forested or agricultural watersheds. Species composition, species richness, and total density all recovered within one year for over 70% of systems studied. Lotic fish communities were not resilient to press disturbances (e.g., mining, logging, channelization) in the absence of mitigation efforts (recovery time >5 to >52 yr) and in these cases recovery was limited by habitat quality. Following pulse disturbances, autecological factors, site-specific factors, and disturbance-specific factors all affected rates of recovery. Centrarchids and minnows were most resilient to disturbance, while salmonid populations were least resilient of all families considered. Species within rock-substrate/nest-spawning guilds required significantly longer time periods to either recolonize or reestablish predisturbance population densities than did species within other reproductive guilds. Recovery was enhanced by the presence of refugia but was delayed by barriers to migration, especially when source populations for recolonization were relatively distant. Median population recovery times for systems in which disturbances occurred during or immediately prior to spawning were significantly less than median recovery times for systems in which disturbances occurred immediately after spawning. There was little evidence for the influence of biotic interactions on recovery rates.     

Assessing the Potential for Salmon Recovery via Floodplain Restoration: A Multitrophic Level Comparison of Dredge-Mined to Reference Segments

Pre-restoration studies typically focus on physical habitat, rather than the food-base that supports aquatic species. However, both food and habitat are necessary to support the species that habitat restoration is frequently aimed at recovering. Here we evaluate if and how the productivity of the food-base that supports fish production is impaired in a dredge-mined floodplain within the Yankee Fork Salmon River (YFSR), Idaho (USA); a site where past restoration has occurred and where more has been proposed to help recover anadromous salmonids. Utilizing an ecosystem approach, we found that the dredged segment had comparable terrestrial leaf and invertebrate inputs, aquatic primary producer biomass, and production of aquatic invertebrates relative to five reference floodplains. Thus, the food-base in the dredged segment did not necessarily appear impaired. On the other hand, we observed that off-channel aquatic habitats were frequently important to productivity in reference floodplains, and the connection of these habitats in the dredged segment via previous restoration increased invertebrate productivity by 58%. However, using a simple bioenergetic model, we estimated that the invertebrate food-base was at least 4× larger than present demand for food by fish in dredged and reference segments. In the context of salmon recovery efforts, this observation questions whether additional food-base productivity provided by further habitat restoration would be warranted in the YFSR. Together, our findings highlight the importance of studies that assess the aquatic food-base, and emphasize the need for more robust ecosystem models that evaluate factors potentially limiting fish populations that are the target of restoration.     

Habitat Improvements and Fish Community Response Associated with an Agricultural Two‐Stage Ditch in Mower County,Minnesota

Water quality and stream habitat in agricultural watersheds are under greater scrutiny as hydrologic pathways are altered to increase crop production. Ditches have been traditionally constructed to remove water from agricultural lands. Little attention has been placed on alternative ditch designs that are more stable and provide greater habitat diversity for wildlife and aquatic species. In 2009, 1.89 km of a conventional drainage ditch in Mower County, Minnesota, was converted to a two‐stage ditch (TSD) with small, adjacent floodplains to mimic a natural system. Cross section surveys, conducted pre‐ and post‐construction, generally indicate a stable channel with minor adjustments over time. Vegetation surveys showed differences in species composition and biomass between the slopes and the benches, with changes ongoing. Longitudinal surveys demonstrated a 12‐fold increase in depth variability. Fish habitat quality improved with well‐sorted gravel riffles and deeper pool habitat. The biological response to improved habitat quality was investigated using a Fish Index of Biological Integrity (FIBI). Our results show higher FIBI scores post‐construction with scores more similar to natural streams. In summary, the TSD demonstrated improvements in riparian and instream habitat quality and fish communities, which showed greater fish species richness, higher percentages of gravel spawning fish, and better FIBI scores. This type of management tool could benefit ditches in other regions where gradient and geology allow.     

Changes in Streambed Composition in Salmonid Spawning Habitat of the Elwha River during Dam Removal

One uncertainty associated with large dam removal is the level of downstream sediment deposition and associated short‐term biological effects, particularly on salmonid spawning habitat. Recent studies report downstream sediment deposition following dam removal is influenced by proximity to the source and river transport capacity. The impacts of dam removal sediment releases are difficult to generalize due to the relatively small number of dam removals completed, the variation in release strategies, and the physical nature of systems. Changes to sediment deposition and associated streambed composition in the Elwha River, Washington State, were monitored prior to (2010‐2011) and during (2012‐2014) the simultaneous removal of two large dams (32 and 64 m). Changes in the surface layer substrate composition during dam removal varied by year and channel type. Riffles in floodplain channels downstream of the dams fined and remained sand dominated throughout the study period, and exceeded levels known to be detrimental to incubating salmonids. Mainstem riffles tended to fine to gravel, but appear to be trending toward cobble after the majority of the sediment was released and transported through system. Thus, salmonid spawning habitats in the mainstem appear to have been minimally impacted while those in floodplain channels appear to have been severely impacted during dam removal.     

Establishing and using study criteria to ensure the rigor and robustness of survival compliance testing at hydroelectric dams

An elaborate set of criteria have been developed by fish managers and regulators to assure the accuracy, precision, representativeness, and robustness of survival compliance studies coordinated within the Federal Columbia River Power System in the northwestern USA. Dam passage survival, defined as survival from the dam face to the tailrace mixing zone, must be ≥96 % for spring out migrating juvenile salmonids [i.e., yearling Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss)] and ≥93 % for summer outmigrants (i.e., subyearling Chinook salmon). Survival must be estimated with a standard error ≤1.5 %. However, these quantitative benchmarks are only part of a multifaceted set of criteria, including representative dam operations, river discharge levels, and fish selection, along with tests of model validity that must be satisfied. These criteria are illustrated using acoustic-tag survival compliance studies conducted at The Dalles Dam on the Columbia River, 2010–2012. The results suggest evaluation criteria for survival compliance tests must balance the needs for rigor and robustness with the ability to reasonably perform the tests in naturally varying riverine systems.