Fish Habitat Use Research Articles

Quarry rock reef design features influence fish assemblage structure across a systematically heterogenous restoration reef

To restore an area of temperate rocky-reef degraded by sedimentation, scour, and burial, a large quarry rock reef, the Palos Verdes Restoration Reef (PVR), was built with a heterogenous design including high relief elements intended to increase fish biomass productivity and support a diverse reef community. The replicated design features provide a unique opportunity to study the effects of reef design on fish habitat use patterns. To determine how submodule scale habitat features are associated with variation in the assemblage structure of eleven focal fish species on the PVR we conducted diver-operated stereo-video surveys on all 18 PVR modules 9–13 months after construction. The highest mean densities of most focal fish species and highest total fish densities were observed on high and medium-relief reef submodules and their adjacent ecotones positioned on the offshore sides or ends of modules. These included the most abundant species on the PVR, the zooplanktivorous Blacksmith (Chromis punctipinnis), as well as the fishery species Kelp Bass (Paralabrax clathratus) and California Sheephead (Bodianus pulcher). On the inshore side of parallel modules, the reef and ecotone transects on low and medium relief submodules exhibited the lowest total mean fish densities, and consistently lower mean focal fish species densities. Focal fish species assemblages also differed between the reef and sand-rock ecotone transects. Reef-resident planktivorous fishes likely contribute to reef primary and secondary productivity through consumer mediated nutrient transport and are an important consideration in restoration reef design. Future reef restoration designs should consider incorporating replicated heterogeneous design features including the placement of higher relief elements relative to shore and current patterns as a special consideration for providing habitat for planktivorous reef-resident fishes.

Drivers of variability in surf zone habitat use by sandy beach fish: Unwitting citizen scientists reveal detailed spatiotemporal patterns

Surf zones of sandy beaches are among the most heavily impacted aquatic ecosystems, yet are of critical ecological importance for inshore fish and fisheries. Knowledge of the drivers of fish habitat use in surf zones is needed across broad scales to advise conservation and fisheries management, but sampling capabilities can be limited in spatio-temporal extent and resolution. The lesser weever Echiichthys vipera is a small, benthic, venomous fish that dominates surf zone fish assemblages in Northwest Europe and inflicts painful stings on beachgoers. This study capitalises on an extensive record of E. vipera sting incidents to characterise variations in surf zone habitat use in relation to key physical environmental factors. Sting incidents, standardised by water user numbers, are used as a proxy for E. vipera abundance across 77 beaches throughout Southwest England, with 2 h resolution, from April–November 2018. General Additive Models indicated a clear peak in E. vipera abundance at spring low tides, in the afternoons of summer months, under calmer wave conditions and at higher levels of solar irradiance. Although the order of significance differed, human water users were also driven by the same variables, compounding sting interactions over time. Key physical variables did not explain spatial variation in E. vipera abundance, although there was a weak relationship with sea surface temperature, and some evidence that reflective beaches are unsuitable. Physical factors explained more spatial variation in human water users, who gathered at more dissipative beaches with greater wave heights. This detailed study of an important surf zone fish reveals clear drivers of temporal variation in habitat use, yet infers wide suitability of beaches varying in the key physical drivers of sandy shore ecology.

Seasonal habitat use and diel vertical migration in female spurdog in Nordic waters

BackgroundStudying habitat use and vertical movement patterns of individual fish over continuous time and space is innately challenging and has therefore largely remained elusive for a wide range of species. Amongst sharks, this applies particularly to smaller-bodied and less wide-ranging species such as the spurdog (Squalus acanthias Linnaeus, 1758), which, despite its importance for fisheries, has received limited attention in biologging and biotelemetry studies, particularly in the North-East Atlantic.MethodsTo investigate seasonal variations in fine-scale niche use and vertical movement patterns in female spurdog, we used archival data from 19 pregnant individuals that were satellite-tagged for up to 365 days in Norwegian fjords. We estimated the realised niche space with kernel densities and performed continuous wavelet analyses to identify dominant periods in vertical movement. Triaxial acceleration data were used to identify burst events and infer activity patterns.ResultsPregnant females frequently utilised shallow depths down to 300 m at temperatures between 8 and 14 °C. Oscillatory vertical moments revealed persistent diel vertical migration (DVM) patterns, with descents at dawn and ascents at dusk. This strict normal DVM behaviour dominated in winter and spring and was associated with higher levels of activity bursts, while in summer and autumn sharks predominantly selected warm waters above the thermocline with only sporadic dive and bursts events.ConclusionsThe prevalence of normal DVM behaviour in winter months linked with elevated likely foraging-related activity bursts suggests this movement behaviour to be foraging-driven. With lower number of fast starts exhibited in warm waters during the summer and autumn months, habitat use in this season might be rather driven by behavioural thermoregulation, yet other factors may also play a role. Individual and cohort-related variations indicate a complex interplay of movement behaviour and habitat use with the abiotic and biotic environment. Together with ongoing work investigating fine-scale horizontal movement as well as sex- and age-specific differences, this study provides vital information to direct the spatio-temporal distribution of a newly reopened fishery and contributes to an elevated understanding of the movement ecology of spurdog in the North-East Atlantic and beyond.Graphical

Year-round sampling of the fish community in a boreal lake: differences between summer and winter influence estimates of species composition, catch, and fish size.

Boreal lakes experience pronounced seasonal variation in abiotic factors, especially light, temperature, and oxygen. A deep boreal humic lake was sampled year-round to test putative changes in total fish catch, species composition, catch-per-unit-effort (CPUE), habitat use, fish size, and condition. Monthly sampling was conducted in Lake Pääjärvi, southern Finland, during one full year in 2020-2021 as well as in March and August 2021 and 2022. The fish community was dominated by cyprinid species in all months, but the percentage of percid fish caught increased during the warm summer period. Most fish were caught in littoral habitats and the highest catches occurred in summer, but some species (e.g., ruffe, Gymnocephalus cernua, and pikeperch, Sander lucioperca) remained abundant in the winter catch. The body size of fish was larger in the winter catch, while condition factor was higher in summer for most species. Fish species proportions in total catch, CPUE, and average size of fish were closest to the annual mean values in September, which may be used as the optimal period to monitor fish communities of similar deep boreal lakes. Our findings highlight the need for year-round research to reveal the impacts of rising temperatures and diminishing ice-covered periods in fish communities and lake food webs.

Spawning migration and habitat characteristics of Labeobarbus species in the Gumara River and its tributaries, Lake Tana subbasin, Ethiopia

Information on the spawning migration and habitat use of migratory fish is critical to protect and restore threatened or endangered populations. Twenty-two individuals of three species, namely Labeobarbus platydorsus, L. megastoma, and L. truttiformis, were implanted with radio tags to study their spawning migration in the Gumara River and its tributaries between July and October of 2018 to 2021. Fourteen individuals were found at least twice throughout their migration, eleven moved upstream up to 41.0 and 44.4 river kilometers (rkm), and three were tracked when moving downstream. The upstream spawning movement of the tagged fish lasted 9 to 27 days, and their ground speeds ranged from 0.07 to 1.50 km h-1. The habitat use of untagged Labeobarbus specimens in the spawning sites was also assessed using fyke nets, cast net fishing, and data from fishermen’s catches. Labeobarbus truttiformis mainly exploited the Kizen tributary stream with gravel substrates and less turbid water for spawning. Several small-sized individuals of L. megastoma spawned in the Wonzuma and Dukalit tributaries. By contrast, larger-sized specimens of L. platydorsus and L. megastoma spawned in the main river channel at the riffles and the gravel/pebble size substrate. Destructive fishing using gillnet dragging, filtering, and damming/fencing has recently intensified at the spawning areas (~ 41.0 rkm to 45.0 rkm), which likely affects spawning populations. Therefore, we recommend that fishing in the main river channel and tributaries must be banned during the months of August, September, and October to safeguard and conserve the threatened Labeobarbus species.

Bioecology of Electric Fish (Actinopterygii: Gymnotiformes)

The poraquê has an elongated and cylindrical body, with just one anal fin, which extends across almost the entire abdomen it resembles the shape of an eel. Its head is flat and its mouth is equipped with a row of sharp, conical teeth. The color of this animal is always very dark, but the ventral part of the body is yellowish and they have poor vision. This group of fish is known for their ability to generate and detect electrical fields in the environment in which they occur, and these characteristics are used in communication, prey detection, defense, reproduction and even to help these animals move in the absence of light. This manuscript aims to describe the biology, ecology, morphology, geographic distribution, life cycle, habitat, and therapeutic use of electric fish (Chordata: Actinopterygii: Gymnotiformes). Concerned with establishing a public profile of quality research in the area, we sought to answer these questions based on a literature review in the main journals (national and international) classified by the Coordination for the Improvement of Higher Education Personnel (CAPES). Complement this analysis with other documents such as books, theses, dissertations, scientific journals, documents, and digital platforms.

Movements and habitat use of native and invasive piscivorous fishes in a temperate and channelized lowland river

AbstractLowland temperate rivers provide important habitats for piscivorous fishes, but with their year-round spatial and temporal habitat use is often poorly understood, including their use of off-channel habitats. Here, the movements and habitat use of the piscivorous native Northern pike Esox lucius and invasive pikeperch Sander lucioperca were investigated using acoustic telemetry in the highly regulated (through impoundment) lower River Severn, Western England over a 12-month period, where off-channel habitat availability was limited to a single boat marina. The movements of both species varied with season and temperature, with both species moving greater distances in spring. Increasing water temperatures up to 15 °C resulted in a higher frequency of movements of both species, but movements then decreased at temperatures higher than this. Northern pike detections in the river increased in periods of lower river discharge and warmer temperatures, with the off-channel refuge providing an important habitat all year round (78% of detections occurred there). While 63% of pikeperch detections also occurred in the marina, 89% of these detections occurred between December and April. These results thus emphasise the importance of this limited off-channel habitat as potential spawning locations for invasive pikeperch and foraging areas for native Northern pike.

Into the wild: coupling otolith and archival tag records to test assumptions underpinning otolith chemistry applications in wild fish

Chronological records of elemental concentrations in fish otoliths are a widely used tool to infer the environmental conditions experienced by individual fish. To interpret elemental signals within the otolith, it is important to understand how both external and internal factors impact ion uptake, transport and incorporation. In this study, we have combined chronological records from otoliths and archival data storage tags to quantify the influence of internal (sex, size, age, growth) and external (temperature, depth, salinity) conditions on otolith elemental chemistry of cod (Gadus morhua) in natural settings of the Baltic Sea. This study focused on elements primarily under physiological control: Phosphorus (P), magnesium (Mg) and zinc (Zn); and elements under environmental control: Strontium (Sr), barium (Ba) and manganese (Mn). Based on known spatial and temporal patterns in environmental conditions and fish size, growth, and maturity, we posed a series of hypotheses of expected otolith element patterns. Partial effects of internal and external drivers on element concentration were analyzed using a Linear Mixed Model approach with random variables (fish and year). Predicted effects of otolith concentrations of all elements under physiological control (P, Mg, Zn) showed similar trends, with distinct seasonal patterns (lowest concentration in late spring, highest concentrations in winter), and a positive correlation with water temperature, in addition to higher Zn and lower P in spawning individuals. Predicted effects of otolith concentrations of elements expected to be predominantly under environmental control showed the predicted geographic and depth-related trends based on ambient salinity (Ba) and coastal hypoxia (Mn). However, contrary to expectation, Sr was unrelated to salinity. Predicted otolith Ba, Sr and Mn concentrations also exhibited pronounced seasonal patterns that were out of phase with each other but appeared to be partly explained by spawning/feeding migrations. While performing laboratory validation studies for adult fish is typically not possible, these results highlight the importance of assessing local water chemistry and freshwater endmembers in one’s study system before otolith elemental chemistry can be reliably used to reconstruct fish habitat use and environmental histories.

Fish community, seasonal movement and habitat use in a subtropical coastal lagoon

Coastal lagoons are environmentally and naturally dynamic areas crucial for fish reproduction and nursery. Thus, this research aims to evaluate the importance of the species performing their biological processes and development in this ecosystem. For this purpose, a subtropical coastal lagoon in the Gulf of California was taken as a case study, where four sampling seasonal campaigns were performed within the lagoon (internal zones) and the marine environment (external) nearby zones from 2016 to 2017. Diversity, evenness, and dominance indices were determined, and the number of individuals, size, length at first maturity, and reproductive period of each species were analyzed to obtain fish use of the lagoon. This coastal lagoon shows a high abundance of juvenile organisms in the cold season, whereas mature adults were mostly present during the warm season. Environmental variables influencing fish species development and distribution, such as sea surface temperature, salinity, and chlorophyll-a, were detected. To conclude, the subtropical coastal lagoon in the Gulf of California is an important nursery area where reproduction occurs mostly near adjacent areas.

Effect of 12 mm PIT tags on the survival, growth, and ecologically significant behaviours of juvenile critically endangered endemic Zingel asper

Understanding the movement ecology and habitat use of freshwater fish is crucial for their conservation, with telemetry being an essential tool. Current tagging methods are restricted by the minimum body size of fish, as tags should not exceed 2% of the fish's body mass. This limitation hinders the study of juvenile small-bodied endangered species, as the reduced fitness of tagged individuals can negatively impact their populations. This study examines the feasibility of using 12-mm PIT tags on juvenile and subadult individuals (63–90 mm fork length) of the critically endangered Rhône streber, Zingel asper. Results indicate that tagging does not significantly affect survival, growth or behavioural traits, despite the tag weight being between 2.2% and 5.4% of the fish's weight. Tag retention was 100%, with 90% of individuals having the PIT tag fully encapsulated in the body cavity wall after 55 days. The only possible negative effect observed was a tendency, albeit statistically non-significant, for slower escape velocity in the smallest tagged individuals. These findings reduce the known minimum body size limit for 12-mm PIT tags for this species. However, the smallest individuals may be more sensitive to tagging, warranting careful consideration to avoid potential negative impacts on wild populations.

Spatio-temporal dynamics of habitat use by fish in a restored alluvial floodplain over two decades

River floodplain channels can serve as reproduction, nursery or refuge areas for fish. Although the complementary use of floodplain and main channels is known, few studies attempted to quantify this use and even fewer analysed its controlling factors. The objectives of this study are (1) to describe the spatio-temporal use of floodplain habitats and to identify their roles as complementary habitats for fish and (2) to analyse how abiotic variations and their modifications under restoration impact habitat use by fish. To meet these objectives, we analysed (Principal Components Analysis and Coinertia Analysis) multi-site data collected over 20 years in eight main channels and 23 floodplain channels of eight restored sectors of the French Rhône River. Results show that habitat use by fish is mainly related to spatial effects, with 37 % of within-sector variance in taxonomic assemblages explained by the stations. As expected, rheophilic species were more abundant in lotic stations and limnophilic species in lentic ones. In addition, we identified an euryecious guild, grouping young of the year taxa (roach, gudgeon, chub, bleak) that used all types of habitats and particularly lentic floodplain channels with short life-span. Temporal effects (with ~10 % of the variance explained by years) combine (1) the effect of restoration, that increased the diversity of fish assemblages across the floodplain, with stronger changes in floodplain channels whose connectivity regime was modified, (2) the effect of high flows on fish habitat use, that reinforces the nursery and refuge functions of floodplain channels. Our results demonstrate the importance of restoring the diversity of habitats and connectivity because floodplain habitats have complementary functions for fish. Furthermore, our results also suggest to account for temporal variations in order to better estimate the potential effects of restoration on river and their floodplains.

The search to identify the fish species chorusing along the Southern Australian Continental Shelf

Fish produce sound to support life functions. Some species produce choruses, vocalizing continuously over a prolonged period, significantly raising background sound levels within a characteristic frequency band. Fish choruses demonstrate distinctive spatiotemporal patterns, the identification of which can provide information on fish distribution, spawning behaviors, habitat use, and responses to environmental and anthropogenic stressors. Many fish choruses have been reported in Australian waters, yet, very few source species have been identified. Analysis of previously collected acoustic recordings was undertaken to identify fish chorus presence along the southern Australian continental shelf. Three fish chorus types were identified with frequencies centered at approximately 1000, 2300, and 350 Hz. Acoustic recorders and unbaited underwater video recorders were then deployed simultaneously in an attempt to identify the source species of these fish choruses. The 1000 and 2300 Hz fish choruses were detected on the acoustic recordings, corresponding with video recordings of large aggregations of Red Snapper (Centroberyx gerrardi) and Deep Sea Perch (Nemadactylus macropterus). This pilot study was the first step in an attempt to develop an effective methodology that could be used to identify the source species of fish choruses present in offshore environments.

Strontium isotope analysis of otoliths reveals differences in the habitat salinity among three sympatric stickleback species of the genus Pungitius.

The analysis of otolith Sr isotope ratios (87Sr/86Sr) is a powerful method to study fish migration in freshwater areas. However, few studies have applied this method to study fish movement in brackish-water environments. Furthermore, despite the fact that habitat differentiation has been shown to drive genetic differentiation and reproductive isolation among stickleback fish, no studies have used the otolith 87Sr/86Sr ratios to analyze habitat differentiation between stickleback ecotypes and species. In this study, we analyzed the otolith 87Sr/86Sr ratios of three sympatric stickleback species of the genus Pungitius in the Shiomi River on Hokkaido Island, Japan: P. tymensis, the brackish-water type of the P. pungitius-P. sinensis complex, and the freshwater type of the P. pungitius-P. sinensis complex. First, we created a mixing equation to depict the relationship between habitat salinity and the 87Sr/86Sr ratios of river water. We found that the otolith 87Sr/86Sr ratios differed significantly among the three species, indicating that the three species utilize habitats with different salinities: P. tymensis and the brackish-water type inhabit freshwater and brackish-water environments, respectively, with the freshwater type using intermediate habitats. In addition, we found that some freshwater individuals moved to habitats with higher salinities as they grew. Our study demonstrates that the analysis of otolith 87Sr/86Sr ratios is a useful method for studying the habitat use of fish in brackish-water environments and habitat differentiation among closely related sympatric and parapatric species.

Modelling migratory behaviour and habitat use of fish in a large, uninterrupted river network: A case study of a migratory salmonid

AbstractBull trout (Salvelinus confluentus) research has historically focused on highly impacted systems or occurred in a reactionary manner following overharvest. Here, we used telemetry and multi‐state capture–recapture modelling to inform management decision‐making for this highly migratory, conservation‐listed species in British Columbia's upper Fraser River watershed (UFW). Our work reduced critical information gaps surrounding the seasonal migration patterns, distribution, and survival rates of fluvial bull trout within the region. By using results of an existing microsatellite DNA analysis, we were able to assign each tagged individual to one of five spawning populations. This assignment allowed us to investigate potential differences in migratory behaviour and seasonal habitat use among the different spawning populations. We identified that the majority of tagged UFW fluvial bull trout made repeated, long‐distance migrations (>300 km one direction) to appropriate spawning, overwintering and foraging habitats. The five populations did not vary in their seasonal transition probabilities at the spatial scale investigated, suggesting key habitats are important to multiple populations. We also detected post‐spawning migration and distribution patterns that suggest UFW bull trout exploit seasonal resource pulses during salmon smolt outmigration. Our results highlight the importance of protecting, restoring and maintaining a diverse assemblage of complex habitats and the natural connections between them (e.g. between tributary spawning habitats and larger rivers) at a spatial scale that supports migratory bull trout life histories. This work provides valuable information for prioritizing conservation actions and identifying restoration opportunities both in the UFW and across the species' range.

Exploitation shifted trophic ecology and habitat preferences of Mediterranean and Black Sea bluefin tuna over centuries

AbstractDuring recent decades, the health of ocean ecosystems and fish populations has been threatened by overexploitation, pollution and anthropogenic‐driven climate change. Due to a lack of long‐term ecological data, we have a poor grasp of the true impact on the diet and habitat use of fishes. This information is vital if we are to recover depleted fish populations and predict their future dynamics. Here, we trace the long‐term diet and habitat use of Atlantic bluefin tuna (BFT), Thunnus thynnus, a species that has had one of the longest and most intense exploitation histories, owing to its tremendous cultural and economic importance. Using carbon, nitrogen and sulphur stable isotope analyses of modern and ancient BFT including 98 archaeological and archival bones from 11 Mediterranean locations ca. 1st century to 1941 CE, we infer a shift to increased pelagic foraging around the 16th century in Mediterranean BFT. This likely reflects the early anthropogenic exploitation of inshore coastal ecosystems, as attested by historical literature sources. Further, we reveal that BFT which migrated to the Black Sea–and that disappeared during a period of intense exploitation and ecosystem changes in the 1980s–represented a unique component, isotopically distinct from BFT of NE Atlantic and Mediterranean locations. These data suggest that anthropogenic activities had the ability to alter the diet and habitat use of fishes in conditions prior to those of recent decades. Consequently, long‐term data provide novel perspectives on when marine ecosystem modification began and the responses of marine populations, with which to guide conservation policy.

Fish habitat use in the Upper Beni mountain streams (Amazon Basin, Bolivia)

Fish habitat use in the Upper Beni mountain streams (Amazon Basin, Bolivia)

Predicting Pacific cod thermal spawning habitat in a changing climate

Abstract Warming temperatures elicit shifts in habitat use and geographic distributions of fishes, with uneven effects across life stages. Spawners and embryos often have narrower thermal tolerances than other life stages, and are thus particularly sensitive to warming. Here, we examine the spatiotemporal variability of thermal spawning habitat for Pacific cod in the eastern Bering Sea. Specifically, we use bottom temperatures from downscaled global climate models coupled with an experimentally-derived hatch success and temperature relationship to predict how the spatial extent, mean latitude, and consistency of thermal spawning habitat has varied over time. Predictions are validated with observations of spawning adults and early larvae. We find that habitat availability has not increased in the past but is predicted to increase and shift northward in the future, particularly if no climate change mitigation occurs. Habitat hotspots are consistent across shorter time periods but do shift across the shelf by the end of the century such that highly suitable areas in the past and present are not predicted to be suitable in the future. This work highlights the importance of coupling experimental data with climate models to identify the complex and mechanistic dynamics among temperature, life histories, and ecology, particularly under climate change.

Seasonal habitat use of yellow perch Perca flavescens in a north‐temperate lake

AbstractKnowledge of species‐specific fish biology, ecology, and habitat use is critical for informing science‐based management. Yellow perch Perca flavescens are an ecologically and recreationally important fish species. Yet, for many north‐temperate systems (e.g. inland lakes of Wisconsin), little is known about yellow perch seasonal habitat use and ecology. We characterised yellow perch seasonal spatial distribution, size–structure, and condition between littoral and pelagic habitats in Crystal Lake (Vilas Co., WI) during the open water period of 2021. Seasonal spatial distribution and population size–structure were characterised by contemporaneous sampling in littoral and pelagic habitats using mini‐fyke nets and vertical gill nets, respectively. Relative abundance estimates for yellow perch in the littoral zone were greatest during early spring and declined throughout the open water season. Yellow perch pelagic relative abundance estimates were lowest in spring, peaked at the onset of stratification, and then declined and remained relatively consistent throughout the open water season. In general, yellow perch population size–structure and condition were greatest in the pelagic zone. Our findings suggest that after spring spawning, larger yellow perch prefer/select pelagic habitats, while sub‐adults and juveniles prefer/select littoral habitats, potentially resulting from increased predator refugia and(or) resource availability. Our results emphasise the importance of evaluating gear and fishery assessment bias, particularly when the target species may use a range of habitat types within a system.

Assessing the Effects of Physical Barriers and Hypoxia on Red Drum Movement Patterns to Develop More Effective Management Strategies

Human modification of coastal ecosystems often creates barriers to fish movement. Passive acoustic telemetry was used to quantify movement patterns and habitat use of red drums (Sciaenops ocellatus) within and around a complex of coastal impoundments, and explored how the presence of artificial structures (i.e., bollards and culverts) and a hypoxia-related mortality event impacted fish movement. Results indicated bollards impede the movement of individuals with head widths greater than the mean distance between bollards (~16.0 cm). Red drum home range area and daily distance traveled were related to water dissolved oxygen concentrations; as oxygen levels decreased, fish habitat use area decreased initially. However, continued exposure to hypoxic conditions increased fish cumulative daily distance traveled. When exposed to anoxic waters, fish daily distance traveled and rate of movement were greatly reduced. These findings suggest prolonged exposure to low dissolved oxygen in combination with artificial structures can reduce movement of red drum, increase risk of mortality, and decrease habitat connectivity. Constructing and maintaining (sediment and biofouling removal) larger culvert openings and/or using wider bollard spacing would improve water circulation in impoundments, increase habitat connectivity, and facilitate movement of large sportfish inhabiting Florida’s coastal waters.

Predicting biomass of resident kōkopu (Galaxias) populations using local habitat characteristics.

With the global decline of freshwater fishes, quantifying the body size-specific habitat use of vulnerable species is crucial for accurately evaluating population health, identifying the effects of anthropogenic stressors, and directing effective habitat restoration. Populations of New Zealand's endemic kōkopu species (Galaxias fasciatus, G. argenteus, and G. postvectis) have declined substantially over the last century in response to anthropogenic stressors, including habitat loss, migratory barriers, and invasive species. Despite well-understood habitat associations, key within-habitat features underpinning the reach-scale biomass of small and large kōkopu remain unclear. Here, we investigated whether the total biomass of large (> 90 mm) size classes of each kōkopu species and the composite biomass of all small (≤ 90 mm) kōkopu were associated with components of the physical environment that provided refuge and prey resources across fifty-seven 50-m stream reaches. Because kōkopu are nocturnal, populations were sampled by removal at night using headlamps and hand-nets until reaches were visually depleted. Based on Akaike's information criterion, greater large banded kōkopu biomass was most parsimoniously explained by greater pool volume and forest cover, greater large giant kōkopu biomass by greater bank cover and pool volume, and greater large shortjaw kōkopu biomass by greater substrate size and pool volume. In contrast, greater composite small kōkopu biomass was best explained by smaller substrate size, reduced bank cover, and greater pool volume. Local habitat associations therefore varied among kōkopu species and size classes. Our study demonstrates the importance of considering the ontogenetic shift in species' habitat use and provides an effective modelling approach for quantifying size-specific local habitat use of stream-dwelling fish.