Food web analyses offer useful insights into understanding how species interactions, trophic relationships, and energy flow underpin important demographic parameters of fish populations such as survival, growth, and reproduction. However, the vast amount of food web literature and the diversity of approaches can be a deterrent to fisheries practitioners engaged in on‐the‐ground research, monitoring, or restoration. Incorporation of food web perspectives into contemporary fisheries management and conservation is especially rare in riverine systems, where approaches often focus more on the influence of physical habitat and water temperature on fish populations. In this review, we first discuss the importance of food webs in the context of several common fisheries management issues, including assessing carrying capacity, evaluating the effects of habitat change, examining species introductions or extinctions, considering bioaccumulation of toxins, and predicting the effects of climate change and other anthropogenic stressors on riverine fishes. We then examine several relevant perspectives: basic food web description, metabolic models, trophic basis of production, mass‐abundance network approaches, ecological stoichiometry, and mathematical modeling. Finally, we highlight several existing and emerging methodologies including diet and prey surveys, eDNA, stable isotopes, fatty acids, and community and network analysis. Although our emphasis and most examples are focused on salmonids in riverine environments, the concepts are easily generalizable to other freshwater fish taxa and ecosystems.

We examined riparian system responses to an extreme rainfall event on 1–4 December 2007, in eleven small watersheds (mean area—13.2 km2) from 2008–2016 at debris flow, high flood, and low flood reaches (all extended overbank flows). Macroinvertebrate responses followed expected outcomes after extreme disturbance including increasing chironomids and other multi-voltine species. A core assemblage of twenty abundant and common species-maintained populations even after debris flow (likely by recolonizing quickly) with total richness during project of 253 including 183 rare species (<0.01 total abundance) supporting an annual turnover of species from 22 to 33%. Primary disturbance changes to habitat were declines in shade and in-channel wood at all reaches, more strongly at debris flow reaches. Macroinvertebrate communities across disturbance intensities became increasingly similar after the storm. Combined effects of the flood reducing channel complexity and previous logging decreasing in-channel wood recruitment from riparian systems, limits habitat complexity. Until this feature of forested watershed streams returns, there appears to be a ceiling on reach scale aquatic biological diversity.

Headwater streams and wetlands are integral components of watersheds that are critical for biodiversity, fisheries, ecosystem functions, natural resource-based economies, and human society and culture. These and other ecosystem services provided by intact and clean headwater streams and wetlands are critical for a sustainable future. Loss of legal protections for these vulnerable ecosystems would create a cascade of consequences, including reduced water quality, impaired ecosystem functioning, and loss of fish habitat for commercial and recreational fish species. Many fish species currently listed as threatened or endangered would face increased risks, and other taxa would become more vulnerable. In most regions of the USA, increased pollution and other impacts to headwaters would have negative economic consequences. Headwaters and the fishes they sustain have major cultural importance for many segments of U.S. society. Native peoples, in particular, have intimate relationships with fish and the streams that support them. Headwaters ecosystems and the natural, socio-cultural, and economic services they provide are already severely threatened, and would face even more loss under the Waters of the United States (WOTUS) rule recently proposed by the Trump administration.

We examined how the growth rate and food consumption of juvenile Coho Salmon Oncorhynchus kisutch varied in relation to natural turbidity regimes in a coastal stream of northern California. Instream sensors were used to continuously monitor the location, turbidity, and temperature exposure of juvenile Coho Salmon fitted with passive integrated transponder tags. We observed that overwinter growth rate and food consumption varied in relation to the duration and magnitude of turbidity and temperature exposure. Growth rate and food consumption were positively associated with low-to-moderate turbidity exposures that ranged from >3 NTU to >20 NTU and negatively associated with elevated turbidity exposures that ranged from > 55 NTU to >150 NTU. This shift to negative associations for fish that experienced long exposures at turbidity levels > 55 NTU suggests a threshold for assessing potential risk of impairment. However, our analyses show that the influence of turbidity on consumption and growth rate is complicated by a fish's temperature exposure history, which varies among fish depending on individual movement patterns and duration of residency within different stream reaches. Consequently, Coho Salmon growth reflects the net effect of turbidity, temperature, and other environmental factors that are associated with specific life history patterns. These findings advance our understanding of how natural turbidity regimes may influence Coho Salmon growth and offer insight for assessing biological impairment in streams. Moreover, our findings indicate how knowledge of environmental context is crucial for understanding the applicability of laboratory-derived turbidity thresholds for fish populations in streams. Such findings corroborate other field-based studies and add to evidence that laboratory-derived turbidity thresholds alone may be inadequate predictors of biological impairment to stream fish populations.

We analyzed data sets from the Caspar Creek Watershed study, with a 55-year comprehensive record of hydrologic regime in two sub-watersheds with different logging treatments, and three separate instream biologic studies conducted since 1990. Long-term data sets of instream biota are rare, and we used them to investigate sediment regime response to forest harvest and extremes in flow regime. Increases in sediment transport after logging were observed in the North Fork during second experiment at Caspar Creek in the 1990’s. Our analysis found turbidities were higher after logging across the range of flows including high magnitude/short duration as well as low magnitude/long duration events. However, few sediment impacts to macroinvertebrate assemblages were observed above and below tributaries with upstream harvest. Specifically, there were no differences in presence/absence of sediment sensitive taxa before and after logging. Moreover, North and South Forks sensitive taxa distributions were similar. With the South Fork, we compared 2016 and 2017 macroinvertebrate assemblages collected in July and May respectively. Statistical classification separated South Fork communities clearly by year and watershed location, reflecting a dynamic community. A six-grouping solution of 81 taxa divided based on relative abundance, watershed distribution, and functional feeding group. Natural disturbance has been high in the watershed recently with discharge regime varying five-fold since 2014, a drought year, and with higher than normal winter flooding in 2017. Sediment sensitive taxa were distributed in two groups of the six and showed no distinguishable patterns. However, overall patterns of the whole macroinvertebrate community structure between years and watershed locations were observed in the classification.

Timber harvest has many effects on aquatic ecosystems, including changes in hydrological, biogeochemical, and ecological processes that can influence mercury (Hg) cycling. Although timber harvest's influence on aqueous Hg transformation and transport are well studied, the effects on Hg bioaccumulation are not. We evaluated Hg bioaccumulation, biomagnification, and food web structure in 10 paired catchments that were either clear-cut in their entirety, clear-cut except for an 8-m wide riparian buffer, or left unharvested. Average mercury concentrations in aquatic biota from clear-cut catchments were 50% higher than in reference catchments and 165% higher than in catchments with a riparian buffer. Mercury concentrations in aquatic invertebrates and salamanders were not correlated with aqueous THg or MeHg concentrations, but rather treatment effects appeared to correspond with differences in the utilization of terrestrial and aquatic basal resources in the stream food webs. Carbon and nitrogen isotope data suggest that a diminished shredder niche in the clear-cut catchments contributed to lower basal resource diversity compared with the reference of buffered treatments, and that elevated Hg concentrations in the clear-cut catchments reflect an increased reliance on aquatic resources in clear-cut catchments. In contrast, catchments with riparian buffers had higher basal resource diversity than the reference catchments, indicative of more balanced utilization of terrestrial and aquatic resources. Further, following timber harvest THg concentrations in riparian songbirds were elevated, suggesting an influence of timber harvest on Hg export to riparian food webs. These data, coupled with comparisons of individual feeding guilds, indicate that changes in organic matter sources and associated effects on stream food web structure are important mechanisms by which timber harvest modifies Hg bioaccumulation in headwater streams and riparian consumers.

Land-use activities can alter hydrological and biogeochemical processes that can affect the fate, transformation, and transport of mercury (Hg). Previous studies in boreal forests have shown that forestry operations can have profound but variable effects on Hg export and methylmercury (MeHg) formation. The Pacific Northwest is an important timber producing region that receives large atmospheric Hg loads, but the impact of forest harvesting on Hg mobilization has not been directly studied and was the focus of our investigation. Stream discharge was measured continuously, and Hg and MeHg concentrations were measured monthly for 1.5 years following logging in three paired harvested and unharvested (control) catchments. There was no significant difference in particulate-bound Hg concentrations or loads in the harvested and unharvested catchments which may have resulted from forestry practices aimed at minimizing erosion. However, the harvested catchments had significantly higher discharge (32%), filtered Hg concentrations (28%), filtered Hg loads (80%), and dissolved organic carbon (DOC) loads (40%) compared to forested catchments. MeHg concentrations were low (mostly <0.05 ng L-1) in harvested, unharvested, and downstream samples due to well-drained/unsaturated soil conditions and steep slopes with high energy eroding stream channels that were not conducive to the development of anoxic conditions that support methylation. These results have important implications for the role forestry operations have in affecting catchment retention and export of Hg pollution.

The Calapooia River in western Oregon supports a small winter steelhead trout (Oncorhynchus mykiss) population and historically supported spring Chinook salmon (Oncorhynchus tshawytscha). Early timber harvesting removed the riparian forest, and log transportation practices simplified the channel. Those disturbance legacies continue to affect fish habitat by limiting shade and channel complexity, complicating conservation efforts. To evaluate juvenile salmonid rearing potential, macroinvertebrate drift, thermal regime and physical habitat were measured at eight sites in 24km of the upper river during late summer baseflow. Overall physical habitat was simple, with few functioning instream structures or pools. During the 22-day drift study, flows declined and maximum site stream temperatures ranged from 23.1 degrees C at the lower end to 16.4 degrees C 24km upstream. Macroinvertebrate drift concentrations ranged from 0.7-13.7 ind. m(-3) with biomasses from 0.02-1.23mg m(-3). Drift concentration biomass was higher upstream (P=0.006) than downstream and declined overall (P<0.001) during the study. Drift biomass was dominated by five taxon groups - Baetis tricaudatus, Calineuria californica, Hesperoperla pacifica, Simulium spp., and Chironomidae, which were 65% of total biomass. During twilight, total biomass and biomass of B. tricaudatus, Simulium spp., and Chironomidae (both larvae and adults) were higher. Total drift declined dramatically over the study period owing to decreases in drift concentration and a 58% decline in discharge, greatly reducing overall drift and available food resources for juvenile-rearing salmonids. The upper catchment, both with cooler temperatures and higher food availability, provided the best conditions for juvenile anadromous salmonids to survive late summer conditions. Conservation consequences of climate change-induced alterations in flow and temperature may further affect habitat quality for juvenile salmonids in this catchment in the coming decades.

Glyphosate, aminomethylphosphonic acid (AMPA), imazapyr, sulfometuron methyl (SMM), and metsulfuron methyl (MSM) were measured in streamwater collected during and after a routine application of herbicides to a forestry site in Oregon's Coast Range. Samples were collected at 3 stations: HIGH at the fish-no-fish interface in the middle of the harvest and spray unit, MID at the bottom of the unit, and LOW downstream of the unit. All herbicides were applied by helicopter in a single tank mix. AMPA, imazapyr, SMM, and MSM were not detected (ND) in any sample at 15, 600, 500, and 1000ng/L, respectively. A pulse of glyphosate peaking at approximately equal to 62ng/L manifested at HIGH during the application. Glyphosate pulses peaking at 115ng/L (MID) and 42ng/L (HIGH) were found during the first 2 postapplication storm events 8 and 10 days after treatment (DAT), respectively: glyphosate was less than 20ng/L (ND) at all stations during all subsequent storm events. All glyphosate pulses were short-lived (4-12h). Glyphosate in baseflow was approximately equal to 25ng/L at all stations 3 DAT and was still approximately equal to 25ng/L at HIGH, but ND at the other stations, 8 DAT: subsequently, glyphosate was ND in baseflow at all stations. Aquatic organisms were subjected to multiple short-duration, low-concentration glyphosate pulses corresponding to a cumulative time-weighted average (TWA) exposure of 6634ng/Lxh. Comparisons to TWA exposures associated with a range of toxicological endpoints for sensitive aquatic organisms suggests a margin of safety exceeding 100 at the experimental site, with the only potential exception resulting from the ability of fish to detect glyphosate via olfaction. For imazapyr, SMM, and MSM the NDs were at concentrations low enough to rule out effects on all organisms other than aquatic plants, and the low concentration and (assumed) pulsed nature of any exposure should mitigate this potential. Integr Environ Assess Manag 2017;13:396-409. (C) 2016 SETAC

The Oregon Coast landscape displays strong spatial patterns in air temperature, precipitation, and geology, which can confound our ability to detect relationships among land management, instream conditions, and fish at broad spatial scales. Despite this structure, we found that a suite of immutable or intrinsic attributes (e.g., reach gradient, drainage area, elevation, and percent weak rock geology of the catchments draining to each of our 423 study reaches) could explain much of the variation in pool surface area across the landscape and could contribute to an estimate of how many juvenile coho salmon (Oncorhynchus kisutch) one might expect to find in those pools. Further, we found evidence of differences in pool surface area across land ownership categories that reflect differing management histories. Our results also suggest that historical land and river management activities, in particular splash dams that occurred at least 50 years ago, continue to influence the distribution of juvenile coho salmon and their habitats today.

Aquatic biological diversity in Pacific Northwest (PNW) forests was examined after two disturbance types: natural (flooding with and without associated debris flows); and anthropogenic (canopy removal).Within the region two multi-decade studies on aquatic insects in western Oregon establish the likely upper ends of forested stream richness, with richness values of ≈300 taxa collected at Berry Creek and 449 taxa within a small watershed (Lookout Creek, 6400 ha).Therefore, compared to intensively studied sites, at least 100 to 200 species have not been documented at these sites.We examine disturbance impacts on assemblage richness in the PNW with data from three studies characterized by similar levels of sampling and taxonomic effort.Rare species were important contributors to richness, as 20 to 30% of taxa within each study area were found at only one site.Mature, clearcut, high flow, and debris flow disturbance states were compared.Ephemeroptera (p=<0.001)richness increased after debris flows and high flows, and Chironomidae (p=0.04)increased after debris flows and clearcutting.Site variability was high, with assemblage structure weakly clustered by disturbance severity as debris flow disturbance (characterized by both streambed and canopy removal) mostly separated from high flow and clearcut disturbances.

Six channel-spanning boulder weirs with other associated structural configurations were constructed along mainstem of Mosby Creek in 2011 to improve fish habitat. The structures were studied to evaluate their influence on water temperatures and their stability against hydraulic forces across a range of boulder sizes in different configurations. Boulders were configured as weirs, clusters, duos, barbs, and individuals, with mean volumes 1.4, 0.45, 0.42, 0.83, and 0.63 m(3), respectively. Bankfull widths ranged from 9.1 to 12.2 m, with stream gradients between 0.8 and 1.2%. After summer construction, 671 boulders were surveyed and then resurveyed following winter flows. There were five high flow events during the first winter, with two above the 2-year recurrence interval. The weirs captured approximately 1200 m(3) of alluvium after the first winter. Only minor movement of boulders was observed, with only seven moving > 10 m, and all weirs were intact. Boulders of similar density (mass/volume) in these flow conditions should be stable once boulder volume exceeds 0.5 m(3). Three noteworthy findings were seen in the temperature analysis. Lower absolute maxima temperatures were observed directly below weirs. There was no change upstream or downstream of weirs, signifying that thermal change is local. Thirdly, maximum minima were similar following alluvial deposition, indicating little effect of daylight heat gain. While created hyporheic zones may have little stream-wide influence, small areas of cool water are thermal refugia for fish, particularly in systems where current temperatures can stress salmonids. Boulder weirs show promise as a method that develops such habitats.

E nvironmental resource managers have long recognized the im- portance of protecting water quality to safeguard human health and ecological resources.In North America, the Soil Conservation District movement, initiated in 1935 with passage of the Soil Conservation Act, represents early interest in this goal (Ice 2004).The 1948 Federal Water Pollution Control Act (Ch.758; P.L. 845) and subsequent amendments (e.g., the 1972 Federal Water Pollution Control Act or "Clean Water Act" [CWA] and amendments) authorized other federal, state, and local entities to prepare programs that would reduce pollution of interstate waters and tributaries and improve the condition of surface and underground waters. 1 The CWA makes a distinction between point and nonpoint sources."The term point source means any discernible, confined and discrete conveyance, including but not limited to any pipe, ditch, channel, tunnel, conduit, well, discrete fissure, container, rolling stock, concentrated animal feeding operation, or vessel or other floating craft, from which pollutants are or may be discharged.This term does not include agricultural stormwater discharges and return flows from irrigated agriculture" (33 USC § 1362).Point sources are subject to regulation and control through permit requirements of the National Pollution Discharge Elimination System (NPDES) (33 USC § 1342)."Nonpoint sources" (NPS) of water pollution are those that do not meet the definition of a point source.The US Environmental Protection Agency's (EPA) NPS web page states that NPS pollution "comes from many diffuse sources" and "generally results from land runoff, precipitation, atmospheric deposition, drainage, seepage or hydrologic modification." 2 The CWA directs the states to establish NPS pollution management programs and, with technical assistance from the EPA, to develop and implement best management practices (BMPs) for reducing pollutant loadings from NPS (33 USC § 1329).The EPA has defined most forestry activities as NPS [40 CFR § 122.27(b)(1)], and all states with significant levels of forest management activities have developed and implemented forestry NPS control programs (National Council for Air, and Stream Improvement, Inc. [NCASI] 2009).BMPs are a primary approach in these

We compared stream ecosystem responses to two types of disturbances: flood and debris flows. A large storm in February 1996 disturbed four similarly sized sub‐watersheds of the Calapooia River, in the Cascade Mountains of Oregon, USA. All sub‐watersheds had flood and in two, 31 and 81% of the perennial channel, a debris flow affected the channel. For 8 years, we used a suite of approaches: stream temperature, nutrient regime, periphyton and macroinvertebrate assemblages, and resident trout abundance and habitat to evaluate the persistence of instream impacts. Differences in stream temperatures and nitrate‐nitrogen concentrations were evident, probably, due to the removal of vegetation and modification of riparian soils at the debris flow sites. Instream biological responses varied. After the event, fish, including trout, were rare with no fish at the debris flow sites. Within 6 years, trout densities ( Oncorhynchus mykiss and Oncorhynchus clarki ) were similar and young‐of‐the‐year trouts were common. In contrast, periphyton and macroinvertebrate assemblages differed. Periphyton biomass was lower and nitrogen‐fixing periphyton was more abundant at the debris flow sites. Macroinvertebrate assemblage diversity was higher at the debris flow sites due to fewer dominant taxa. Macroinvertebrate functional feeding groups also differed with fewer gatherers and more scrapers at the debris flow sites. Debris flow impacts related to loss of riparian canopy will probably persist until mature red alder stands are re‐established along stream‐reaches affected by debris flows to provide nitrogen input and shade. Copyright © 2011 John Wiley & Sons, Ltd.

The Fine Sediment Biotic Index (FSBI) is a regional, stressor-specific biomonitoring index to assess fine sediment (<2 mm) impacts on macroinvertebrate communities in northwestern US streams. We examined previously collected data of benthic macroinvertebrate assemblages and substrate particle sizes for 1,139 streams spanning 16 western US Level III Ecoregions to determine macroinvertebrate sensitivity (mostly at species level) to fine sediment. We developed FSBI for four ecoregion groupings that include nine of the ecoregions. The grouping were: the Coast (Coast Range ecoregion) (136 streams), Northern Mountains (Cascades, N. Rockies, ID Batholith ecoregions) (428 streams), Rockies (Middle Rockies, Southern Rockies ecoregions) (199 streams), and Basin and Plains (Columbia Plateau, Snake River Basin, Northern Basin and Range ecoregions) (262 streams). We excluded rare taxa and taxa identified at coarse taxonomic levels, including Chironomidae. This reduced the 685 taxa from all data sets to 206. Of these 93 exhibited some sensitivity to fine sediment which we classified into four categories: extremely, very, moderately, and slightly sensitive; containing 11, 22, 30, and 30 taxa, respectively. Categories were weighted and a FSBI score calculated by summing the sensitive taxa found in a stream. There were no orders or families that were solely sensitive or resistant to fine sediment. Although, among the three orders commonly regarded as indicators of high water quality, the Plecoptera (5), Trichoptera (3), and Ephemeroptera (2) contained all but one of the species or species groups classified as extremely sensitive. Index validation with an independent data set of 255 streams found FSBI scores to accurately predict both high and low levels of measured fine sediment.

Drifting invertebrates from small headwater streams are a food subsidy for fishes and other downstream consumers in larger streams. This subsidy can become especially important for stream fishes during summer due to high metabolic demand caused by elevated water temperatures. The source length in small streams contributing these drifting invertebrates to fish bearing habitat has not been established. We conducted an experiment to determine if summer drift delivered by headwater streams to larger channels is influenced by contributions originating more than 100 m upstream. We conducted this experiment on tributaries of the Calapooia River, Oregon, USA. We blocked drift with 250 pm mesh nets in three streams 100 m upstream of our sample nets continuously for 48 d. We also sampled five streams without blocking nets. Four 24 h samples of drift were collected prior to the placement of blocking nets and every two weeks afterwards at each stream. Overall mean abundance and mean biomass of drift did not differ between blocked and unblocked streams for any sampling period. There was a temporal trend at all sites of declining invertebrate abundance and biomass. We found no treatment effect for any of the most common insect orders or for the 16 genera that comprised at least 1 % of the total organisms captured. The majority of invertebrate drift is of local origin in headwater streams during summer baseflow.

We measured winter thermal characteristics longitudinally in four third-order streams, two each in the Idaho Batholith and Blue Mountain ecoregions. From November to April we measured temperature along 3.7 km to 11.9 km of stream at six to eight sites. Streams were snow covered for most of the winter. There was a seasonal pattern of stream-wide cooling in November and warming in April at all streams. In the mid-winter months (December, January, and February), the sites in the Blue Mountain streams had mean monthly maxima ranging from 0.2 to 3.0 degrees C and minima -0.1 to 1.5 degrees C stream-wide, whereas both Idaho Batholith streams were near 0.0 degrees C throughout their length and had monthly ranges of 0.2 degrees C or less. Winter temperature differences between streams of the two ecoregions create substantial differences in cumulative degree-days which could be a factor in the structure of instream biotic communities.