The impact of an introduced predator on a threatened galaxiid fish is reduced by the availability of complex habitats

1. The availability of complex habitats such as macrophytes may be vital in determining the outcomes of interactions between introduced predators and native prey. Introduced brown trout (Salmo trutta) have impacted numerous small native freshwater fishes in the southern hemisphere, but the potential role of complex habitats in determining the direct outcomes of brown trout – native fish interactions has not been experimentally evaluated. 2. An in‐lake enclosure experiment was used to evaluate the importance of structurally complex habitats in affecting the direct impacts of brown trout on a threatened galaxiid fish. Five Galaxias auratus and a single brown trout were added to enclosures containing one of three different habitat types (artificial macrophytes, rocks and bare silt substrate). The experiment also had control enclosures without brown trout. Habitat‐dependence of predation risk was assessed by analysis of G. auratus losses to predation, and stomach contents of remaining fish were analysed to determine if brown trout directly affect the feeding of G. auratus and whether this is also habitat‐dependent. 3. Predation risk of G. auratus differed significantly between habitat types, with the highest mortality in enclosures with only bare silt substrate and the lowest in enclosures containing artificial macrophytes. This result highlights the importance of availability of complex habitats for trout – native fish interactions and suggests that increasing habitat degradation and loss in fresh waters may exacerbate the direct impacts of introduced predators. 4. Stomach contents analyses were restricted to fish in enclosures with artificial macrophytes and rocks, as most fish were consumed in enclosures with brown trout and only bare silt substrate. These analyses suggest that brown trout do not directly affect the feeding of G. auratus in complex habitats, but it is still unknown whether its feeding is reduced if complex habitats are unavailable.     

Assessing the suitable habitat for reintroduction of brown trout (Salmo trutta forma fario) in a lowland river: A modeling approach

Huge efforts have been made during the past decades to improve the water quality and to restore the physical habitat of rivers and streams in western Europe. This has led to an improvement in biological water quality and an increase in fish stocks in many countries. However, several rheophilic fish species such as brown trout are still categorized as vulnerable in lowland streams in Flanders (Belgium). In order to support cost‐efficient restoration programs, habitat suitability modeling can be used. In this study, we developed an ensemble of habitat suitability models using metaheuristic algorithms to explore the importance of a large number of environmental variables, including chemical, physical, and hydromorphological characteristics to determine the suitable habitat for reintroduction of brown trout in the Zwalm River basin (Flanders, Belgium), which is included in the Habitats Directive. Mean stream velocity, water temperature, hiding opportunities, and presence of pools or riffles were identified as the most important variables determining the habitat suitability. Brown trout mainly preferred streams with a relatively high mean reach stream velocity (0.2–1 m/s), a low water temperature (7–15°C), and the presence of pools. The ensemble of models indicated that most of the tributaries and headwaters were suitable for the species. Synthesis and applications. Our results indicate that this modeling approach can be used to support river management, not only for brown trout but also for other species in similar geographical regions. Specifically for the Zwalm River basin, future restoration of the physical habitat, removal of the remaining migration barriers and the development of suitable spawning grounds could promote the successful restoration of brown trout.     

Changes in the Georgian Bay fish community,with special reference to lake trout (Salvelinus namaycush) rehabilitation

We describe and explain some of the changes in the fish community as reflected by the catches of the commercial fishery, and evaluate the efforts to restore the trout (Salvelinus spp.) in Georgian Bay. The changes in the fish community were caused in part by excessive fishing for lake trout (S. namaycush), lake whitefish (Coregonus clupeaformis) and deepwater ciscoes (Coregonus spp.), and the introduction of new species such as sea lamprey (Petromyzon marinus), alewife (Alosa pseudoharengus), rainbow smelt (Osmerus mordax) and salmonids (Oncorhynchus spp.). The most striking changes were the near extinction of the lake trout, reductions in lake herring (Coregonus artedii), deepwater ciscoes and lake whitefish, and the increase in abundance of smelt and alewife. In an effort to replace the loss of yield from the cold-water habitat, a fast growing and early maturing hybrid trout (splake [S. namaycush × S. fontinalis]) and its backcross to lake trout were selectively bred for stocking in Georgian Bay. Splake did poorly because of low survival immediately after planting. The survival of backcross after planting was better, but adult mortality was still high. Adult survival of backcross improved considerably after restrictions were placed on the commercial fishery in 1984. The first naturally produced backcross larvae were collected in 1985.     

Multiple lines of evidence reveal complex rainbow trout responses to stream habitat enhancements

1. Habitat enhancements seek to ameliorate the detrimental effects of environmental degradation and take many forms, but usually entail structural (e.g. logs, cribs, reefs) or biogenic (e.g. carrion additions, vegetation plantings, fish stocking) augmentations with the intent of increasing fish annual production (i.e. accrual of new fish biomass through time). Whether efforts increase fish production or simply attract fish has long been subject to debate.
2. Streams of the Pacific Northwest are commonly targeted for habitat enhancements to mitigate for the detrimental effects of dams and other forms of habitat degradation on Pacific salmon. Nutrient mitigation (i.e. the practice of artificially fertilising freshwaters) is a form of biogenic habitat enhancement that attempts to mimic the enrichment effects of a natural Pacific salmon spawning event. This approach assumes nutrient augmentations alleviate nutrient limitation of primary producers and/or food limitation of primary and secondary consumers, culminating in increased fish production.
3. We conducted a multi-year manipulative experiment and tracked responses of interior rainbow trout (Oncorhynchus mykiss) to annual additions of Pacific salmon carcasses as part of an effort to enhance the productivity of salmonid populations in streams where salmon runs have been lost. We employed an integrated approach to partition the mechanisms driving numerical responses of trout populations across timescales, to assess population turnover, and to track responses to habitat enhancements across individual to population level metrics.
4. Short-term numerical increases by trout were shaped by immigration and subsequently via retention of individuals within treatment reaches. As trout moved into treated stream reaches, individuals foraged, grew, and subsequently moved to other locations such that short-term increases in fish numbers did not persist from year to year. All told, additions of salmon carcasses alleviated apparent food limitation and thereby increased secondary production of rainbow trout. However, at an annual time scale, increased production manifested as larger individual fish, not more fish within treated reaches. Fish movements and high population turnover within treated stream reaches apparently led to the subsequent dispersal of increased fish production.
5. We found multiple lines of evidence that indicated that annual additions of salmon carcasses aggregated rainbow trout and enhanced their annual production. Through this replicated management experiment, we documented dynamic individual and population level responses to a form of stream habitat manipulation across weekly and annual timescales.

     

Carotenoids in fish. XX. Carotenoids in Salmo gairdneri rich. And Salmo trutta morpha fario L.

The author investigated the presence of various carotenoids in Salmo gairdneri Rich. and Salmo trutta morpha fario L. from the trout fish farm (artificial food) and from the river as the natural conditions (natural food).The findings of these investigations indicate that the trout bred in natural conditions are richer in carotenoids, provitamins of vitamin A, than are trout from the trout fish farm. In all probability the variety of food available in natural conditions provides better facilities for the accumulation of carotenoids in the body of trout in their natural habitat.     

A comparison of passage efficiency for native and exotic fish species over an artificial baffled ramp

This study used an experimental approach to compare the passage success of native and exotic fish species from the temperate Southern Hemisphere over an artificial baffled fish ramp designed for overcoming low-head (≤1.0 m) fish migration barriers. Passage efficiency was, on average, lower for the exotic species [koi carp (Cyprinus carpio), rudd (Scardinius erythrophthalmus) and rainbow trout (Oncorhynchus mykiss)] compared to the native species [inanga (Galaxias maculatus), redfin bully (Gobiomorphus huttoni) and common bully (Gobiomorphus cotidianus)]. Nonetheless, there was considerable variation between individual species, with rainbow trout outperforming common bully and juvenile inanga, but koi carp and rudd failing to pass any of the ramps. The differences in predicted probability of passage success between the native and exotic fish species in this study were sufficient in some cases to indicate the potential for the baffled fish ramps to operate as a selective migration barrier. Nonetheless, further testing is required to validate these results across a broader range of conditions before deployment.     

Linking movement and reproductive history of brook trout to assess habitat connectivity in a heterogeneous stream network

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Recruitment variation in a stream galaxiid fish: multiple influences on fry dynamics in a heterogeneous environment

1. The relative importance of density‐dependent and density‐independent processes in explaining fluctuations in natural populations has been widely debated. In particular, the importance of larval supply and whether it may control the type of regulatory processes a population experiences has proved contentious. 2. Using surveys and field experiments conducted in streams in Canterbury, New Zealand, we investigated how variation in the survival of non‐migratory Galaxias vulgaris fry was affected by density‐dependent and density‐independent processes and how this variation influenced recruitment dynamics. 3. Fry populations with high settlement densities experienced a 70–80% reduction in population size from density‐related mortality during the first fourteen days after peak settlement but thereafter the influence of density‐dependent processes on fry was weak. The impact of environmental conditions on fry populations was dependent on fry size and the magnitude of the perturbation, such that flooding effects on fry survival were most severe when fry were small. 4. In streams not affected by flooding, the size and density of introduced trout (Salmo trutta and Oncorhynchus mykiss) were the most significant factors determining the abundance of eventual recruits. A field experiment manipulating brown trout access to fry populations revealed that trout as small as 110 mm may be capable of greatly reducing and possibly preventing galaxiid recruitment. 5. Overall, the results indicated density‐dependent population regulation was only possible at sites with high native fish densities because trout were likely to be suppressing the number of potential recruits at sites with low native fish numbers. Whilst density‐dependent processes had a strong effect on fry survival following the period of peak fry abundance, density‐independent processes associated with flow and predatory trout influences on fry survival largely determined recruitment variability among galaxiid populations. Focusing conservation efforts on improving habitat to increase fry retention and reducing the impacts of trout on galaxiids would ensure more native fish populations reached their potential abundance.     

Movement in a large predatory fish: coral trout, Plectropomus leopardus (Pisces: Serranidae), on Heron Reef, Australia

 Movement by the larger more mobile species of coral reef fish plays a significant role in determining patterns in abundance and population structure. Fish movement is also relevant to the use and effectiveness of marine reserves in managing fish populations. Coral trout are large piscivorous serranids supporting major fisheries on the Great Barrier Reef (GBR). This study reports on the within-reef movement of the common coral trout, Plectropomus leopardus, at Heron Reef, southern GBR, over a twelve month period, investigated by tagging and underwater tracking. Tracking of coral trout revealed no apparent relationship between the area moved and stage of tide or time of day. However, movement areas were affected by the size of fish: in spring a linear relationship between fish size and area of movement was measured, but in summer the largest (male) fish moved over significantly smaller areas than medium-sized fish. Movement of males may be related to cleaning behaviour and spawning. Fifty nine percent (n=101) of the tagged fish were resighted over periods of 4–5 months, in “home sites” measuring ∼2000 m². Coral trout were not restricted to home sites, but moved on average 2 km along the reef slope; maximum distances of 7–7.5 km were measured. Coral trout appear to range as mobile, opportunistic predators, but also maintain home sites for access to shelter and cleaning stations. Accepted: 1 August 1996     

Does social status within a dominance hierarchy mediate individual growth,residency and relocation?

The availability of food, and hence energy, is known to influence the abundance, habitat choice and growth of individuals. In contrast, there is a paucity of knowledge on how the interaction of energy supply and social status determines patterns of residency and movement. This study tests whether the presence of conspecifics and an individual’s social status in relation to food supply influence the fitness and movement of a drift-feeding fish (Galaxias fasciatus). Using an information-theoretic approach (AIC), our analysis indicated that the most parsimonious model of fish movement among pools was one that included food supply, social rank and fish relative growth rate. Our results indicated that subordinate fish relocated more frequently compared to dominant fish, most likely as a consequence of intra-specific competition that limited the access of these smaller fish to resources and constrained their growth. Our results suggest that energy constraints may force individuals to explore new habitats in an effort to find more energetically profitable patches. We conclude that intra-specific competition mediated through the social hierarchy amongst closely interacting individuals plays a key role in determining individual growth, residency and relocation.     

Seascape structure and complexity influence temperate seagrass fish assemblage composition

Understanding how spatial patterning relates to ecological processes is fundamental to define important species–environment associations at broader scales. Analyses targeting habitat structure (i.e. composition and configuration) in terrestrial landscapes are increasing, but similar studies in marine landscapes are still relatively uncommon. In this study, we explored how seascape structure and complexity (determined from significant spatial pattern metrics) influenced summer and autumn fish assemblage composition in 30 seagrass (Zostera marina) meadows along the west coast of Sweden. Species density was not influenced by seascape structure in any season. In contrast, the majority of significant fish assemblage variables were influenced by seascape structure during the summer (i.e. abundance and proportion of juveniles, abundance of Labridae and abundance of occasional shallow‐water visitors) whilst fewer in the autumn (i.e. abundance of occasional shallow‐water visitors and Synganthidae). For instance, less complex seascapes were more suitable for juvenile assemblages in summer, as these seascapes exhibit larger patch sizes of appropriate habitat (e.g. Z. marina) and less edge boundaries providing refuges from predators and food resources. Abundances of migrating fish, such as the sea trout Salmo trutta, also responded positively to a less complex seascape in the summer though perhaps ecological processes, such as prey availability, were additional contributing factors driving this relationship. High complexity seascapes only had a positive influence on the abundance of taxa using multiple habitats (Labridae during the summer). Our study shows that fish assemblages in temperate marine environments are significantly linked to spatial habitat patterning and seascape complexity. This offers valuable insights into species–habitat–seascape linkages, information important for coastal conservation and marine spatial planning.     

Movements of brown trout, Salmo trutta, and juvenile Atlantic salmon, Salmo salar, in a coastal stream in northern Norway

Movements of resident brown trout (age 2+ to 9+ years) and young Atlantic salmon (age 1+), stocked as fry, were studied in July, August and September in a coastal stream in northern Norway. Between 85 and 89% of the brown trout were recaptured in the study area (346m, 1326m²) within 45m of their release point throughout the investigation period. Most specimens had moved less than 150m. Trout movements were related to local variation in density. Trout occupying those sections of stream with the lowest fish densities (5.3–10.9 fish 100m^?2) had a significantly lower movement rate than fish from sections with densities between 13.7 and 31.5 fish 100m^?2. Trout that moved from their marking section were significantly larger than specimens that did not leave their original site. There was a significant correlation between permanence of station each month and the mean water level that month. The majority of the trout (47%) were caught at undercut stream banks or at sites in the proximity of these. A decrease in water level during the study period resulted in a high loss (36%) of such habitat, probably forcing some individuals to move. The recapture data indicate that the trout population consists of one small (c. 15–20%) mobile, and one large sedentary component. Young salmon displayed high station permanence in July and August (93% and 96%). However, in the autumn they exhibited a significant downstream movement, and only 73% were recaptured within their release section. This movement was significantly higher for larger specimens, and is thought to occur because of a pre-winter change in habitat, initiated by a decline in stream temperature. In contrast to trout, salmon in sections containing the lowest densities (22.0–25.0 fish 100m^?2) did not show significantly lower movement rates when compared with salmon at higher densities (32.2–46.3 and 51.8–60.6 fish 100m^?2). The spatial distribution of young salmon indicated the formation of territorial mosaics over the stream bed, which are thought to reduce intraspecific competition.     

Differential responses by two closely related native fishes to restoration actions

Globally, river degradation has decimated freshwater fish populations. To help reverse this trend in a southeastern Australia river, we used multiple restoration actions, including reintroduction of instream woody habitat, riparian revegetation, removal of a weir hindering fish movement, fencing out livestock, and controlling riparian weeds. We monitored the responses of native fish at the segment scale (20 km) and reach scale (0.3 km) over 7 years to assess the effectiveness of the different restoration strategies. Two closely related species, Murray cod Maccullochella peeli and trout cod Maccullochella macquariensis, increased at the restored segment compared with the control segment. However, inherent differences between river segments and low sample size hampered assessment of the mechanisms responsible for segment‐scale changes in fish abundance. In contrast, at the reach scale, only M. peeli abundance significantly increased in reaches supplemented with wood. These differential responses by 2 closely related fish species likely reflect species‐specific responses to increased habitat availability and enhanced longitudinal connectivity when the weir improved passage around a fishway. Changes in M. peeli abundance in segments supplemented with and without wood suggest an increase in carrying capacity and not simply a redistribution of individuals within the segment, facilitated the observed expansion. Our findings confirm the need to consider individual fish species' habitat preferences carefully when designing restoration interventions. Further, species‐specific responses to restoration actions provide waterway managers with precise strategies to target fish species for recovery and the potential to predict fish outcomes based on ecological preferences.     

Short-term cues used by foraging trout in a California stream

Stream salmonids choose foraging locations to maximize the energy benefit of foraging within the constraints of size-mediated dominance hierarchies and predation risk. But, because stream habitats are temporally variable, fish must use a search process to monitor changing habitat conditions as a means of locating potentially-better foraging locations. I explored the cues used by the cutthroat trout, Oncorhynchus clarki clarki, when searching for food at the pool scale by artificially increasing prey availability at different locations by using special feeders and by manipulating pool velocities. Behavior of individually marked fish was monitored from stream bank platforms under unmanipulated control conditions and under seven experimental sets of conditions involving different combinations of feeder location and velocity manipulation. Under natural conditions fish elected to forage in the deepest (>50 cm), fastest (0.10–0.25 m s⁻¹) locations and within 1 m of structure cover, but would readily move to shallower (<30 cm) water away from cover if velocities were manipulated to be highest there. Although fish did not locate feeders unless they were placed in high-velocity areas, when high velocity was provided fish would move into very shallow water (<20 cm) if prey were delivered there. Responses of individual trout to manipulations indicated that water velocity was the main physical cue used by fish to decide where to forage, and that fish could also learn about new food sources by observing conspecifics. Overall, results indicated fish were not “perfect searchers” that could quickly locate new food resources over short time scales, even when the new resources were within a few meters of the fish’s normal foraging location. When given the correct cues, however, fish could detect new food sources and defend them against subordinate fish. Movement of new fish into and out of the study pools during the ten-day observation period was common, consistent with the idea that trout used movement as a means of exploring and learning about habitat conditions at the reach scale.     

Fall and Early Winter Movements of Cutthroat Trout, Oncorhynchus clarki, in Relation to Water Temperature and Ice Conditions in Dutch Creek, Alberta

Fall and winter movement and behaviour of 28 cutthroat trout Oncorhynchus clarki was determined using radiotelemetry to evaluate the effects of water temperature and ice conditions. As water temperatures decreased, cutthroat trout moved from more solitary positions to aggregations. With few exceptions, radiotagged fish aggregated with other fish in groups varying from 5 to approximately 70 fish. The percentage of fish aggregating and the mean size of aggregation was negatively correlated with water temperature. The mean distance moved by radiotagged cutthroat trout from 1 September to 12 January was 1.0km. After forming aggregations, fish tended to stay within a 120m length of stream until the end of tracking in mid-January. Fish that were less sedentary after their initial overwintering movement usually moved when their habitat was occluded by anchor ice. These fish moved thirty times farther and six times more often than fish in stable overwintering areas. In Dutch Creek multiple freezing events caused several ice related habitat exclusions and movements associated with large decreases in air temperature. Several bull trout and mountain whitefish were observed in groups with cutthroat trout.     

What predicts the use by brook trout (Salvelinus fontinalis) of terrestrial invertebrate subsidies in headwater streams?

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Rainbow trout <Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis> energetic responsesto pulsed flows in the American River,California, assessed by electromyogram telemetry

Although rainbow trout Oncorhynchus mykiss within the American River, California, apparently exhibit minimal upstream or downstream movements in response to hydroelectric-power-generation-related pulsed flows, the associated energetic costs are unknown. We implanted rainbow trout (n = 9, ≥30 cm SL) with electromyogram (EMG)-sensor-equipped radio transmitters to assess the swimming behavior and associated energetic costs associated with their responses to pulsed flows. Using laboratory calibrations in a Brett-type swimming respirometer, the trouts’ swimming speeds and oxygen consumption rates were estimated for their in-river EMG data, through a complete hydroelectric power-generation river pulsed-flow sequence (pre-pulse, increasing flow, peak, and decreasing flow stages), on several (mean: 3.2) sampling dates. Using a mixed-linear model, we found that fish swimming speed estimates increased during the increasing flow stage, while the associated mean oxygen consumption rates also increased at this stage. At river flows near the usual peak (>44 m³s⁻¹), swimming speeds and movement rates decreased, possibly due to the fish using the river’s habitat complexities as hydraulic cover. We conclude that rainbow trout incur increased swimming-related energetic costs during increasing flows and, potentially, decreased foraging opportunities at high flows.     

Response of stream fish to improved water quality: a comparison between the 1960s and 1990s

1. The effect of improved water quality on fish assemblages in streams in southern Sweden was assessed by comparing species composition at 161 sites and water quality at twenty-nine sites in the 1960s and the 1990s. 2. Water quality had improved and there was an increase in the number of sites or catchments with brown trout (Salmo trutta), stone loach (Barbatula barbatula) and eel (Anguilla anguilla). The response was greatest for brown trout and was best explained by increased oxygen concentrations. 3. The number of sites with nine-spined stickleback (Pungitius pungitius), ide (Leuciscus idus) and brook lamprey (Lampetra planeri) decreased between the 1960s and 1990s. The decrease was greatest for nine-spined stickleback and was related to the increase in sites with trout, suggesting that nine-spined stickleback may be sensitive to predation or competition. 4. Improved water quality has led to recolonization by brown trout, probably enabling biotic interactions to play a larger role in structuring fish assemblages. Improving water quality was an effective method for rehabilitating fish populations in streams where natural colonization was possible.     

Fish predation affects the structure of a benthic community

1. We conducted an experimental study of predation by benthivorous fish on a natural community of stream invertebrates using a reach‐scale approach. Over a 2‐year period (experimental phase), the benthic invertebrate community of a stretch containing two species of benthivorous fish was compared with a fishless stretch. Thereafter, all fish were removed and benthic community structure was analysed again to account for natural differences between the two stretches (reference phase). 2. Benthivorous fish at the moderate densities investigated did not affect total benthic biomass or density, but did alter species composition. In addition, the fish effect differed between pool and riffle habitats, with larger effects in the pools indicating a habitat‐specific predation effect. In the reference phase, when all fish were removed from the stream, the difference between the two stretches was reduced. 3. The benthivorous fish reduced the densities of four taxa (Pisidium sp., Dugesia gonocephala, Gammarus pulex, Limoniidae), representing 29% of total biomass. It is possible that density reductions of other species were masked by prey migration despite the relatively large spatial scale. Indeed, higher drift activity in the upstream fishless stretch could have increased the density of Baetis rhodani in the fish stretch, as indicated by the results of a drift model. 4. Our results provide insights into stream food web ecology because fish predation showed effects even in a natural system where habitat complexity was high, environmental factors were highly variable and many predator and prey species interacted and because benthivorous fish were the focus, whereas the majority of previous predation experiments in streams have used drift‐feeding trout.     

Conflicting effects of woody debris on stream fish populations: implications for management

1. Coarse woody debris (CWD) in stream channels causes changes in flow, sedimentation and ratios of pool to riffle areas. There is a consensus among fishery managers and scientists that CWD is beneficial to stream fish communities because of its enhancement of habitat diversity, invertebrate production and cover. Our hypothesis was that CWD accumulation or introduction would not increase in‐stream habitat capacity for all species and their ontogenic stages at reach and stream scales. 2. The study used a system of gravel‐bed streams with naturally dynamic CWD accumulations and a fish community consisting of Salmo trutta, Cotttus gobio, Phoxinus phoxinus, Lampetra cf planeri, Nemacheilus barbatulus and Anguilla anguilla. Cotttus gobio and L. cf planeri are protected by an EU Directive and S. trutta is exploited for angling. Riffles, pools and CWD matrices, considered as the basic habitat/spatial units of channel structure, were sampled separately and abundance of each fish species quantified seasonally at each spatial scale. 3. Multiple‐pass electric fishing techniques were used. Capture efficiencies were calculated for species, habitat and season. Areal densities (number m^?2) were compared for habitat types and season using nonparametric anova . Canonical analysis and stepwise multiple regression were used to show the most influential physical variables on fish density. Densities were also compared by unit volume (numbers m^?3) for pools and CWD matrices to investigate direct three‐dimensional use for cover. Reach‐scale densities for each fish species in relation to habitat composition were made using Spearman rank correlation of habitat‐scale densities with proportionate areas of the different habitat units in the reach. 4. Habitat‐scale densities of bullheads and age 0+ trout were negatively correlated with depth and CWD areas for some seasons. Densities of lampreys, older trout, eels and minnows were positively correlated with depth in some seasons. Water depth had the most consistent influence on fish abundance at the habitat unit scale. Three‐dimensional comparisons of pools and CWD matrices indicated that only trout older than 1+ may use CWD habitats as cover. 5. Reach‐scale densities of 0+ trout and bullheads were significantly correlated with proportion of riffle area and negatively with CWD and combined CWD‐pool habitat area in the reach. Densities of older trout, large eels and lampreys were positively correlated with CWD area and combined CWD‐pool area in some seasons. Inundation of riffles caused by impoundment upstream of CWD accumulations reduced spawning habitat for trout, bullheads, brook lampreys, minnows and stone loach. A trade‐off was an increase in refugia for older trout, minnows and eels. 6. Coarse woody debris accumulation in streams is not beneficial to all species or ontogenic stages in a mixed species population and could severely limit essential habitat areas for some species. Thus, physical manipulation of channels should be implemented only after a thorough study of the habitat relationships of all species present, especially where protected species coexist with target species. The relative importance of in‐stream morphological changes depends on the spatial and temporal scale of the species life histories.