Periods of extreme flow (i.e., drought and flood) structure aquatic communities, but their effects in hydrologically stable, groundwater-dominated systems (e.g., karst springs) remain poorly understood. These spring systems are often viewed as refugia for endemic fishes. As such, the effects of drought and flooding are thought to be more pronounced than in hydrologically variable systems with the potential to lead to extirpations of endemic fishes. We analyzed a 9-year dataset (2014-2022) from three reaches of the San Marcos River and four reaches of the Comal River, Texas, to evaluate how a major flood and a severe drought influenced habitat structure and fish assemblages among wadeable and non-wadeable areas. Habitat variables were surveyed alongside standardized fish sampling, and fishes were grouped into habitat usage guilds for analysis. Effects of extreme flow periods were similar to the effects reported for hydrologically variable systems in wadeable areas but not in non-wadeable areas. Among wadeable areas, an increase in the amount of algae was detected during drought, but changes to substrates and vegetation coverage because of scouring were not detected following a flood. Also, abundances of pelagic generalist fishes (e.g., Lepomis sp., Herichthys cyanoguttatus) and one species of a pelagic specialist fish (i.e., Astyanax argentatus) decreased following a flood. Unexpectedly, abundances of benthic guild fishes (i.e., Etheostoma sp.) increased during drought and abundances of one species of pelagic specialist fish (Dionda nigrotaeniata) decreased following a flood. Effects of extreme flow periods on habitat structure and fish assemblages in hydrologically stable systems were similar to, or unexpectedly less pronounced, than the effects of flow periods on hydrologically variable systems. These patterns reveal vulnerabilities among generalist species during high flows and drought-associated increases for benthic taxa. These results support ecological theory that groundwater-dominated systems provide resistance to climatic extremes but remain susceptible to community restructuring, with implications for conservation under future climate variability and groundwater extraction.

Assessing ecosystem health in tropical reservoirs requires integrative approaches that capture biological responses in association with physicochemical conditions. In this study, a multimetric ecosystem health assessment framework was developed and applied to evaluate the spatio-temporal ecological status of a tropical reservoir in Southern India. The framework integrates six indicator groups such as fish assemblage structure, fish production, plankton diversity, macrophyte coverage, abiotic water quality, and anthropogenic disturbance, across three reservoir zones (lacustrine, transitional, and riverine) and four seasonal periods. The composite health index indicated an overall good ecological condition (mean score, 63.2%), with pronounced spatial and seasonal variability. The riverine zone exhibited the highest ecological integrity, while transitional zones showed moderate degradation associated with cumulative anthropogenic pressures. Seasonally, ecosystem health peaked during the monsoon and declined markedly during summer, reflecting hydrological stress, elevated temperature, and reduced dissolved oxygen. Fish assemblage and production metrics emerged as the most sensitive indicators of ecosystem condition, whereas abiotic parameters remained relatively stable. The study demonstrates that multimetric frameworks provide a robust and sensitive tool for diagnosing ecological stress in tropical reservoirs and offer practical insights for adaptive fisheries management, habitat restoration, and climate-resilient water resource planning.

Dams and their associated reservoirs have become so ubiquitous on the world's riverscapes that only 23% of rivers now flow freely to the ocean. These artificial structures have known ecological consequences, but ecological studies often suffer from a lack of historical baseline data and uncertainty regarding the degree to which concepts are transferable among altered river systems. We reviewed historical fish assemblage survey data collected over 373km of the upper Sabine River, Texas, USA during 1954-1955, prior to construction of large reservoirs at the upstream and downstream extents of the study area. We then repeated surveys using identical methods in 2023 after reservoirs were in place for multiple decades. The resulting dataset provided opportunity to measure impoundment-driven deviations from historical baseline conditions and test a suite of hypotheses centered on fish assemblage changes across a gradient of proximities (i.e., distances) from reservoirs. We found support for the proximity replacement hypothesis in which fish assemblages nearest to reservoirs experience the highest temporal beta diversity; support for the longitudinal recovery gradient hypothesis in which relative abundance of periodic life history strategists returns to a natural baseline with greater downstream distance from dam tailwaters; support for the proximity host loss hypothesis in which fishes that serve as hosts to Unionid mussels decline in reservoir tailwaters; and support for the proximity host gain hypothesis in which fishes that serve as hosts to Unionid mussels increase in the river-reservoir interface upstream of a dam. This work advances knowledge of ecological consequences associated with dam construction by revealing that concepts developed using space-for-time substitutions (i.e., without historical baseline information) remain pertinent when tested against historical benchmarks and these same concepts are applicable to unstudied systems.

Seagrass beds are vital marine ecosystems that provide habitat and resources for diverse fish communities. This study evaluated the effects of spatial and seasonal seagrass vegetation on fish assemblages inhabiting seagrass ( Zostera marina Linnaeus, 1753) beds around Myeongsa (typically a sandy shore) and Daepo (denser seagrass beds) in the southern coastal region of Geoje Island. Fish samples were collected monthly from September 2009 to November 2010 using a beach seine and push net. A total of 51 fish species (42 species at Myeongsa and 36 species at Daepo) from 31 families were identified across both study sites. The two study sites exhibited distinct seagrass vegetation patterns, with denser seagrass at Daepo and relatively sparse seagrass at Myeongsa. At Myeongsa, Takifugu niphobles (Jordan et Snyder, 1901), Aulichthys japonicus Brevoort, 1862, and Syngnathus schlegeli Kaup, 1856 were the most dominant species (in terms of frequency of occurrence). In contrast, Daepo was dominated by Rudarius ercodes Jordan et Fowler, 1902, Hexagrammos agrammus (Temminck et Schlegel, 1843), and Paracentropogon rubripinnis (Temminck et Schlegel, 1843), highlighting habitat-specific differences between fish assemblages and common fish species. Fish species richness, abundance, and diversity varied substantially depending on habitat type and season. Myeongsa, which was dominated by Takifugu niphobles , had the highest fish abundance, whereas Daepo exhibited a more balanced and diverse species composition. Non-metric multidimensional scaling analysis further demonstrated that habitat and season significantly influenced fish assemblage structure, with seasonal variations in abundance correlating with changes in seagrass biomass and temperature. Our findings provide baseline data for the conservation and management of seagrass-associated fish communities in Korea and contribute to broader efforts to sustain biodiversity within coastal habitats.

We compared fish assemblage structure and total mercury (THg) bioaccumulation between a natural floodplain lake and a constructed irrigation canal in central Brazil. A total of 473 individuals representing 34 species were recorded, and dorsal muscle samples from 62 specimens representing shared species or species occupying comparable trophic positions were analyzed for THg (Curimatella immaculata, Hemiodus microlepis, Astyanax aff. bimaculatus, Triportheus albus, Geophagus sveni, Pimelodus blochii, Pygocentrus nattereri, Lycengraulis batesii, and Cichla kelberi). The floodplain lake exhibited higher species richness, diversity, and evenness, whereas the irrigation canal supported a simplified assemblage dominated by fewer species. Total Hg concentrations were significantly higher in the lake than in the irrigation canal; however, this pattern was observed only for the carnivorous guild (t = 5.384, p < 0.0001) and the detritivorous guild (t = 4.183, p = 0.0001). THg increased significantly with trophic level in both systems, from detritivores to carnivores (F2,4 = 15.127, p = 0.009), yielding comparable trophic magnification slopes (lake: 1.46, 95% CI: 1.11–1.81; canal: 1.36, 95% CI: 0.94–1.77). Despite lower diversity and THg concentrations in the irrigation canal, Hg transfer efficiency across trophic levels was conserved between systems.

Abstract. Syafruddin R, Qamarina MFN, Safuan CDM, Yusuf Y, Afiq-Firdaus AM, Bachok Z. 2026. Spatial and depth patterns of reef fish assemblages in Pulau Tenggol, Malaysia and their links to benthic composition. Biodiversitas 27 (1): d270148. https://doi.org/10.13057/biodiv/d270148. A total of 142 reef fish species (71 genera, 33 families) were recorded at Pulau Tenggol in the South China Sea, Peninsular Malaysia, based on surveys conducted in May 2024 across five stations and three depth strata (5, 10, and 15 m), yielding 12 station-depth transects. Fish assemblages were surveyed using belt transects, while major benthic categories and Hard coral growth-forms composition were quantified using Coral Video Transects and analyzed with Coral Point Count with Excel extensions (CPCe). Fish indices, including fish density, species richness, Shannon diversity, Simpson diversity, and Pielou’s evenness, showed no significant differences among stations or depths (Kruskal-Wallis test, p>0.05), whereas species composition differed significantly across both spatial and depth gradients (PERMANOVA, p>0.05). Major benthic categories and hard coral growth-forms did not differ significantly with depth (p>0.05) but showed significant variation among stations (p>0.05). Mantel tests indicated that fish assemblage structure was significantly associated with hard coral growth-forms (p≤0.05), while no significant correlation was detected with major benthic categories (p>0.05). Fish density was positively correlated with Acropora staghorn/branching growth-forms (ρ: 0.783, p: 0.004, FDR: 0.047; partial ρ: 0.769, p: 0.006, FDR: 0.073) and negatively correlated with encrusting corals (ρ: -0.790, p: 0.004, FDR: 0.047; partial ρ: -0.775, p: 0.005, FDR: 0.073). Healthy hard coral cover was strongly associated with obligate corallivores (ρ: 0.757, p: 0.004, FDR: 0.015; partial ρ: 0.716, p: 0.013, FDR: 0.017) and Chaetodontidae (ρ: 0.669, p: 0.017, FDR: 0.035; partial ρ: 0.616, p: 0.044, FDR: 0.027). Overall, coral health and growth-form complexity were stronger predictors of reef fish assemblage structure than major benthic categories.

Introduction Hydrologic variability is a key driver of ecological structure in lotic systems, shaping habitat conditions, taxonomic diversity, and the functional traits that mediate species’ persistence and performance (e.g., reproductive success). While many studies examine taxonomic responses to variation in flows, few evaluate how spatiotemporal hydrologic variation influences the functional organization within stream fish communities. Methods We quantified seasonal habitat structure and functional trait diversity of fish assemblages across six Ozark Plateau headwater streams representing two contrasting flow regimes: Groundwater Flashy and Runoff/Intermittent Flashy. Fish and habitat data were collected seasonally during a dry year (2002) and a wet year (2003). Functional space was constructed using PCoA of morphological, ecological, and life-history traits, and functional diversity was measured using community weighted means (CWMs), functional richness (FRic), functional evenness (FEve), and functional divergence (FDiv). Results We found that habitat structure differed strongly by flow regime and season, with Runoff/Intermittent streams exhibiting pronounced reductions in depth, area, and velocity, while groundwater streams remained structurally stable. Functional identity of assemblages was similar across flow regimes, dominated by benthic, hydrodynamic taxa with opportunistic and periodic life-history strategies. However, functional structure differed significantly: FEve and FDiv were consistently lower in Runoff/Intermittent Flashy streams in both years, indicating assemblage dominance of species with similar trait combinations and reduced trait partitioning under variable flow. FRic and taxonomic richness remained stable across seasons and flow regimes, suggesting high functional redundancy despite species turnover. Discussion Together, results show that flow regime mediates both habitat structural stability and functional organization. As climatic warming and extreme drought increase hydrologic instability in headwaters, functional trait approaches provide a sensitive tool for detecting losses of functional roles that may not be evident by using taxonomic metrics alone.

Early life stage fishes are susceptible to variation in environmental gradients, which dictate growth and survival, ultimately shaping adult assemblages. Creation of river-reservoir ecosystems (RRE) by impounding rivers results in longitudinal zonation within the reservoir (i.e., riverine, transition, and lacustrine zones) and gradients owing to changes in temperature, flow, turbidity, food availability, and physical structure. We quantified relationships among density, assemblage structure, size structure and daily growth rates of early life stage (ELS) fishes and environmental conditions across zones of eight RRE in central Ohio. We observed significantly higher densities in upstream zones of RRE, correlated with increases in littoral and floodplain habitat (p < 0.001). Fish assemblage structure was similar across zones from river inflows to the dam, but more variable temporally due to seasonal differences in water temperature (p < 0.001), and spawning periodicity. Fish size increased in a downstream direction with smaller individuals in riverine and transition zones and larger individuals in lacustrine zones (p < 0.001). Average growth rates did not differ significantly among zones (p > 0.05) but varied among taxa. Our results demonstrate that high-density nursery areas with more complex habitats do not necessarily correspond with enhanced growth.

Estuarine structure and connectivity influence seasonal and spatial shifts in the food web structure of fish assemblages

Abstract Urban expansion and agricultural activities are primary drivers of degradation in Neotropical streams, affecting their physical integrity and, consequently, their fish assemblages. This study compared fish assemblages between 12 urban and rural streams in the Paranapanema River basin, using a set of 21 ecomorphological indices. Sampling was conducted in April 2019 in 50 m reaches, and ecomorphological data were analyzed using PERMANOVA, NMDS, SIMPER, RDA, functional diversity indices, and null models. PERMANOVA analysis revealed significant differences in the ecomorphological structure of the ichthyofauna ( p = 0.003), corroborated by a clear separation between groups in the NMDS ordination. SIMPER analysis indicated that the pectoral fin aspect ratio, caudal peduncle compression, lateral compression, mouth aspect, and relative caudal peduncle length were the main contributors to the dissimilarity between streams, explaining > 50% of the variation. RDA showed that PPM (suspended solids) was the most significant environmental variable ( p = 0.04) structuring the assemblages. Fish assemblages in urban streams exhibited an ecomorphological pattern with higher values of caudal peduncle compression and relative caudal peduncle, traits adapted for short-distance swimming in turbid waters. In contrast, rural streams, with greater integrity, featured fish with higher lateral compression and pectoral fin aspect ratios, characteristics of structurally complex environments and adapted for higher speed and maneuverability. The results confirm that environmental changes caused by urbanization select for specific morphotypes and highlight the importance of conserving the physical integrity of streams for maintaining the ecomorphological biodiversity of fish communities.

ABSTRACT Aim To investigate how functional traits shape the composition and functional structure of coastal fish assemblages across the four North‐East Atlantic archipelagos, providing insights into the ecological drivers of species distributions and trait patterns in oceanic island systems. Location Four North‐East Atlantic oceanic archipelagos within Macaronesia: the Azores, Madeira, Canary Islands and Cabo Verde. Taxon Coastal marine fishes occurring up to 200 m depth, comprising 682 species. Methods We compiled a validated checklist of coastal fish species (≤ 200 m depth) for each archipelago and integrated these data with a functional trait matrix comprising size category, trophic category, habitat affinity, milieu and climatic affinity. Generalised Linear Models (GLMs) were used to assess the influence of traits on species occurrences. Functional community structure was quantified using six functional diversity indices: functional richness (FRic), evenness (FEve), divergence (FDiv), dispersion (FDis), Rao's quadratic entropy (RaoQ) and FRic intersection (FRic Inter). Model performance was evaluated using AIC, BIC, pseudo R 2 and post hoc comparisons. Trait‐based GLMs were complemented with assemblage‐level RLQ ordination and fourth‐corner tests to evaluate trait–environment coupling while accounting for species co‐occurrence. Results Species richness followed a clear latitudinal gradient, peaking in the Canary Islands and declining towards higher latitudes. RLQ revealed strong global trait–environment co‐structure (Axis 1 = 91.7% of projected inertia), whereas Fourth‐Corner tests detected no individually significant trait–environment associations after Holm correction. RV tests indicated a significant link between trait structure and species composition (Q–L), but not between environmental context and species composition (R–L). Among traits, body size and habitat affinity were the strongest predictors of species occurrences, with larger‐bodied and reef‐associated species more frequent in the southern archipelagos. Functional richness was highest in the Azores, indicating functional distinctiveness despite comparatively low species richness. Incorporating functional diversity indices into GLMs did not improve explanatory power beyond species‐level traits. Main Conclusions Body size and habitat affinity are key determinants of coastal fish assemblages across the Macaronesia archipelagos. Functional diversity peaks in the Azores, while Madeira exhibits intermediate trait compositions between temperate and tropical systems. These patterns provide insight into community assembly mechanisms and may inform predictions of species turnover under future climate change scenarios.

Anthropogenic stressors increasingly threaten freshwater biodiversity, with fish communities particularly sensitive to habitat modification. This study evaluates how river morphological alterations influence fish assemblage structure in 114 mountain rivers of the Southern Carpathians, assessing whether such changes cause species loss or drive shifts toward disturbance-tolerant communities. Using a multi-scale analytical framework integrating non-metric multidimensional scaling, redundancy analysis, and variance partitioning, we quantified the contributions of spatial, catchment, and local habitat variables to community patterns. Spatial- and catchment-scale factors explained the largest variance in fish assemblages (12% in adults and 17% in small-bodied fish). However, morphological pressures proved significant in shaping community structure with clear ecological consequences. Weirs and embankments reduced abundances of rheophilic species (flow-dependent) by 27–38%, potamodromous by 23–42%, invertivorous by 26–49%, benthic by 40–46% and lithophilic taxa by 27–41%, indicating the loss of habitat specialists. In contrast, limnophilic taxa (preferring slow or still water) increased 25 times, phytophilic spawners by 17–41%, and tolerant species by 10%, reflecting biotic homogenization. By integrating a trait-based approach, this study highlights functional shifts that may be overlooked in species-level assessments. It underscores the need to couple local habitat restoration with catchment-scale management to conserve fish biodiversity and maintain natural ecological gradients in mountain river systems.

Amazonian streams are among the most biodiverse freshwater ecosystems, playing a fundamental role in maintaining trophic networks and essential ecological processes. The structure of fish assemblages in these systems is influenced by a combination of environmental and historical factors, including biogeographic and phylogenetic processes. Riparian vegetation and seasonality act as important determinants of species composition in these streams. The objective of this study was to investigate how riparian vegetation integrity and seasonal variation influence the structure and distribution of fish assemblages in Amazonian streams. To this end, samples were collected during different hydrological periods, representing the dry, rainy, and transitional seasons. The methodsused to evaluate fish assemblagesconsidered environmental variables associated with habitat integrity, stream hydrology, and surrounding landscape characteristics. The results revealed that seasonality plays a central role in structuring fish communities, with significant changes in species composition between hydrological periods. Environmental integrity also contributed to patterns of assemblage variation, though to a lesser extent than seasonal changes.

Depth and habitat drive spatial patterns in fish functional diversity: a trait-based assessment across South Africa and southern Mozambique.

Circadian processes are key drivers of animal behaviour, influencing patterns of activity, resource partitioning and competition avoidance. Studies evaluating circadian changes on the structure of marine assemblages are lacking, especially for reef fish. Evaluating the changes imposed by the day-night cycle on the structure and functioning of these assemblages is of critical importance to understand the differences between the diurnal and nocturnal components, as well as the resources they exploit, to better model and manage them. Here, we assessed the fish fauna using an underwater visual census conducted at the same sites during both day and night on a subtropical rocky reef in the Southwestern Atlantic (SWA), aiming to evaluate differences in the community and functional structure of these assemblages. A total of 242 transects were conducted across three sites, with 104 during the day and 138 at night. Fish richness, density, biomass and functional richness were higher in the diurnal period, whereas nocturnal assemblages exhibited higher taxonomic distinctiveness and functional divergence. Both richness and density of nocturnal assemblage, as well as richness and taxonomic distinctness index of the diurnal assemblage, were influenced by depth. The species in each assemblage exhibited different combinations of traits. As expected, diurnal assemblages were richer and occupied a larger proportion of the multidimensional trait space. Body size was comparatively larger for the diurnal assemblage, evidencing niche partitioning based on ontogeny. These results indicate significant differences in the structure of diurnal and nocturnal reef fish assemblages, as expected, driven by resource use, space use and predator avoidance. Fish play a central role in many key processes within reef systems, in addition to their importance for human nutrition and cultural services. Therefore, understanding the components and diversity of nocturnal assemblages is essential to address the significant knowledge gap to understand their role in reef energetics and demand proper management.

The longitudinal gradient prevails over local characteristics in shaping fish species distributions in a large neotropical reservoir

The Yangtze River Estuary is one of the most productive estuarine ecosystems in the western Pacific, supporting diverse fish communities that sustain ecosystem functioning. This study investigated the seasonal patterns and community structure of intertidal fish assemblages to provide a baseline for future habitat assessments. Seasonal surveys conducted from May to December 2024 recorded 47 fish species belonging to 10 orders, 18 families, and 37 genera. Cyprinidae contributed the highest proportion of species (42.55%). Dominant species identified by the index of relative importance-including Cynoglossus gracilis, Coilia nasus, and Lateolabrax japonicus-characterized the seasonal assemblage structure. The assemblages were dominated by sedentary species (82.98%), and demersal fishes accounted for 48.94% of the species. Carnivorous taxa (57.45%) dominated the trophic guilds. Diversity indices indicated moderate diversity (H': 1.797-2.441; C: 0.788-0.892; D: 1.724-4.770; J': 0.6318-0.8642). Similarity analysis based on Jaccard's index (Cj) showed the highest overlap between spring and summer (Cj = 0.5000) and the lowest between spring and winter (Cj = 0.1714); spring-autumn and summer-autumn were approximately 0.30, indicating moderate overlap. ABC curves yielded slightly negative W values in spring and summer and positive values in autumn and winter (W = -0.066 to 0.276), indicating moderately disturbed assemblages in spring-summer and less disturbed communities in autumn-winter. Overall, the study provides a seasonal baseline of intertidal fish assemblages in nearshore waters of the southern branch of the Yangtze River Estuary, which can provide useful ecological context for future assessments of nursery and feeding habitats of juvenile Chinese sturgeon (Acipenser sinensis).

Fish are a key group in any coral community, and their assemblage varies with differences in habitat structure among reefs, as well as with seasonal and interannual environmental fluctuations that influence community structure and ecosystem functioning. Long-term monitoring, combined with taxonomic and functional indexes, can provide valuable information on the effects of local and regional environmental fluctuations on any biological group. This study evaluated the decadal (2013–2022) variability of fish assemblage and their function in a Natural Protected Area composed of a coral community distributed along two islands, using diurnal visual censuses along belt transects (5 transects/site/season/year) in a 3–13 m depth range. The results showed higher values of species richness, functional richness, evenness, and redundancy on Isla Redonda, which also exhibited the highest observed diversity of benthic components, suggesting a potential association between benthic diversity and fish assemblage structure. Throughout the decade, fish assemblages exhibited clear temporal trends influenced by seasonal cycles, large-scale climatic events, and habitat changes. Especially during the El Niño 2015–2016 event, an abnormal increase in temperatures led to marked shifts in species composition and a decline in the abundance of schooling planktivorous species, such as Apogon pacificus. This was followed by a reduction in species richness in 2018, primarily due to habitat homogenization resulting from a decline in benthic diversity. The loss of benthic diversity and more frequent extreme meteorological events will likely disrupt species interactions, affecting coexistence, resource use, and long-term community stability. Although connectivity between islands currently acts as a buffer, this could be compromised if environmental conditions deteriorate (e.g., natural and anthropogenic stressors), causing a significant decline in the reef’s health and provision of ecosystem services.

The construction of new ponds is a widely used mitigation measure in wetland restoration. While fish colonization can compromise their ecological function, knowledge of how frequently, how rapidly, and by which mechanisms fish colonize these habitats is severely limited. In our study of 123 newly created, originally fishless ponds in the Central European agricultural landscape, 58.5% were found to host fish. Fish were already present in 40% of one-year-old ponds and the proportion of non-colonized ponds did not depend on their age. The most common species were the invasive topmouth gudgeon (Pseudorasbora parva) and Prussian carp (Carassius gibelio), along with the native rudd (Scardinius erythrophthalmus). The likelihood of fish colonisation increased with pond area and depth but decreased with the width of littoral vegetation and distance from the nearest settlement, the latter suggesting a strong effect of anthropogenic dispersal. Ponds hosting invasive or stocked fish assemblages exhibited significantly reduced water transparency and submerged macrophyte cover, indicating potential negative impact on their biodiversity. Overall, the study highlights that without effective control of fish dispersal, newly created ponds in agricultural landscape risk losing much of their conservation value and, in some cases, may even facilitate the persistence and spread of invasive species.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-27349-3.

ABSTRACT Environmental changes can have persistent effects on the local and regional dynamics of multispecies assemblages. However, the extent of historical legacies on current diversity patterns may depend on the trajectory and intensity of the environmental change. Here, we investigate how persistent decadal land use and land cover (LULC) changes are related to the taxonomic and functional structure of present‐day fish assemblages in regions with distinct histories of land use transformation. We selected streams in Brazilian river basins where the LULC change has started more than 150 years ago (state of São Paulo), in the 1970s (state of Rondônia), and more intensively in the 2000s (state of Mato Grosso). We used a dataset comprising 219 streams, 240 species, 13 instream variables and 13 variables describing past LULC changes. We used varying‐coefficient models (VCM) to test how instream habitat and past land use are related to taxonomic and functional fish richness and rarity. Although diversity metrics were slightly better explained by instream variables, we found stronger landscape legacy effects on fish diversity in RO and MT, where LULC changes have occurred more recently. We did not detect landscape legacy effects or strong biodiversity–environment relationships in the region that experienced deforestation earliest (SP), probably because fish assemblages are now dominated by generalist species that are more resistant to further environmental change. Our results indicate that landscape legacies may leave more detectable signals in stream communities in regions where the first major LULC changes happened not too long ago. Thus, the influence of past processes on current fish assemblage diversity and structure may decline with increasing time since the initial LULC change. Our study shows that past LULC changes can shape present‐day biodiversity patterns, and that differences in species pool and landscape change histories can lead to different assemblage–environment relationships. Incorporating historical land use variables, especially in recent deforested regions, can therefore improve our understanding of current patterns of biodiversity. Our findings highlight the importance of preserving and restoring riparian corridors to prevent species loss locally and regionally, because, even in long‐altered regions, streams with riparian cover may still support rare species. Overall, integrating land use history and regional context is crucial for effective conservation and biodiversity monitoring in ecosystems, especially those ones under the first major LULC changes.