Alpha and beta diversity of connected benthic–subsurface invertebrate communities respond to drying in dynamic river ecosystems

Drying disturbances are the primary determinant of aquatic community biodiversity in dynamic river ecosystems. Research exploring how communities respond to disturbance has focused on benthic invertebrates in surface sediments, inadequately representing a connected community that extends into the subsurface. We compared subsurface and benthic invertebrate responses to drying, to identify common and context‐dependent spatial patterns. We characterized community composition, alpha diversity and beta diversity across a gradient of drying duration. Subsurface communities responded to drying, but these responses were typically less pronounced than those of benthic communities. Despite compositional changes and in contrast to reductions in benthic alpha diversity, the alpha diversity of subsurface communities remained stable except at long drying durations. Some primarily benthic taxa were among those whose subsurface frequency and abundance responded positively to drying. Collectively, changing composition, stable richness and taxon‐specific increases in occurrence provide evidence that subsurface sediments can support persistence of invertebrate communities during drying disturbances. Beta‐diversity patterns varied and no consistent patterns distinguished the total diversity, turnover or nestedness of subsurface compared to benthic communities. In response to increasing drying duration, beta diversity increased or remained stable for benthic communities, but remained stable or decreased for subsurface communities, likely reflecting contrasts in the influence of mass effects, priority effects and environmental filtering. Dissimilarity between subsurface and benthic communities remained stable or increased with drying duration, suggesting that subsurface communities maintain distinct biodiversity value while also supporting temporary influxes of benthic taxa during drying events. As temporary rivers increase in extent due to global change, we highlight that recognizing the connected communities that extend into the subsurface sediments can enable holistic understanding of ecological responses to drying, the key determinant of biodiversity in these dynamic ecosystems.     

Emerging concepts in temporary‐river ecology

1. Temporary rivers and streams are among the most common and most hydrologically dynamic freshwater ecosystems. The number of temporary rivers and the severity of flow intermittence may be increasing in regions affected by climatic drying trends or water abstraction. Despite their abundance, temporary rivers have been historically neglected by ecologists. A recent increase in temporary‐river research needs to be supported by new models that generate hypotheses and stimulate further research. In this article, we present three conceptual models that address spatial and temporal patterns in temporary‐river biodiversity and biogeochemistry. 2. Temporary rivers are characterised by the repeated onset and cessation of flow, and by complex hydrological dynamics in the longitudinal dimension. Longitudinal dynamics, such as advancing and retreating wetted fronts, hydrological connections and disconnections, and gradients in flow permanence, influence biotic communities and nutrient and organic matter processing. 3. The first conceptual model concerns connectivity between habitat patches. Variable connectivity suggests that the metacommunity and metapopulation concepts are applicable in temporary rivers. We predict that aggregations of local communities in the isolated water bodies of temporary rivers function as metacommunities. These metacommunities may become longitudinally nested due to interspecific differences in dispersal and mortality. The metapopulation concept applies to some temporary river species, but not all. In stable metapopulations, rates of local extinction are balanced by recolonisation. However, extinction and recolonisation in many temporary‐river species are decoupled by frequent disturbances, and populations of these species are usually expanding or contracting. 4. The second conceptual model predicts that large‐scale biodiversity varies as a function of aquatic and terrestrial patch dynamics and water‐level fluctuations. Habitat mosaics in temporary rivers change in composition and configuration in response to inundation and drying, and these changes elicit a range of biotic responses. In the model, aquatic biodiversity initially increases directly with water level due to increasing abundance of aquatic patches. When most of the channel is inundated and most aquatic patches are connected, further increases in aquatic habitat and connectivity cause aquatic biodiversity to decline due to community homogenisation and reduced habitat diversity. The predicted responses of terrestrial biodiversity to changes in water level are the inverse of aquatic biodiversity responses. 5. The third conceptual model represents temporary rivers as longitudinal, punctuated biogeochemical reactors. Advancing fronts carry water, solutes and particulate organic matter downstream; subsequent flow recessions and drying result in deposition of transported material in reserves such as pools and bar tops. Material processing is rapid during inundated periods and slower during dry periods. The efficiency of material processing is predicted to increase with the number of cycles of transport, deposition and processing that occur down the length of a temporary river. 6. We end with a call for conservation and resource management that addresses the unique properties of temporary rivers. Primary objectives for effective temporary river management are preservation or restoration of aquatic‐terrestrial habitat mosaics, preservation or restoration of natural flow intermittence, and identification of flow requirements for highly valued species and processes.     

Evaluating the relationship between basin‐scale fish species richness and ecologically relevant flow characteristics in rivers worldwide

1. River flow alterations due to climate change and increasing water usage affect freshwater biodiversity including fish species richness. Here, we statistically explored the relationships of fish species richness to 14 ecologically relevant flow metrics as well as basin area and latitude in 72 rivers worldwide. 2. The statistical models best supported by the data included three variables with positive coefficients (mean river discharge, basin area and the maximum proportion of no‐flooding period) and three variables with negative coefficients (latitude, coefficients of variation in the frequency of low flow and the Julian date of annual minimum flow). 3. The model outputs have provided the first empirical indication that specific low‐ and high‐flow characteristics may be important in explaining variations in basin‐scale fish species richness. Our findings can be useful in identifying high‐risk basins for conservation of fish species diversity. 4. The results not only support the adoption of mean discharge as a predictor, but also suggest the importance of basin area in predicting basin‐scale fish species richness around the world.     

IRBAS: An online database to collate,analyze, and synthesize data on the biodiversity and ecology of intermittent rivers worldwide

Key questions dominating contemporary ecological research and management concern interactions between biodiversity, ecosystem processes, and ecosystem services provision in the face of global change. This is particularly salient for freshwater biodiversity and in the context of river drying and flow‐regime change. Rivers that stop flowing and dry, herein intermittent rivers, are globally prevalent and dynamic ecosystems on which the body of research is expanding rapidly, consistent with the era of big data. However, the data encapsulated by this work remain largely fragmented, limiting our ability to answer the key questions beyond a case‐by‐case basis. To this end, the Intermittent River Biodiversity Analysis and Synthesis (IRBAS; http://irbas.cesab.org ) project has collated, analyzed, and synthesized data from across the world on the biodiversity and environmental characteristics of intermittent rivers. The IRBAS database integrates and provides free access to these data, contributing to the growing, and global, knowledge base on these ubiquitous and important river systems, for both theoretical and applied advancement. The IRBAS database currently houses over 2000 data samples collected from six countries across three continents, primarily describing aquatic invertebrate taxa inhabiting intermittent rivers during flowing hydrological phases. As such, there is room to expand the biogeographic and taxonomic coverage, for example, through addition of data collected during nonflowing and dry hydrological phases. We encourage contributions and provide guidance on how to contribute and access data. Ultimately, the IRBAS database serves as a portal, storage, standardization, and discovery tool, enabling collation, synthesis, and analysis of data to elucidate patterns in river biodiversity and guide management. Contribution creates high visibility for datasets, facilitating collaboration. The IRBAS database will grow in content as the study of intermittent rivers continues and data retrieval will allow for networking, meta‐analyses, and testing of generalizations across multiple systems, regions, and taxa.     

Mediterranean-climate streams and rivers: geographically separated but ecologically comparable freshwater systems

Streams and rivers in mediterranean-climate regions (med-rivers in med-regions) are ecologically unique, with flow regimes reflecting precipitation patterns. Although timing of drying and flooding is predictable, seasonal and annual intensity of these events is not. Sequential flooding and drying, coupled with anthropogenic influences make these med-rivers among the most stressed riverine habitat worldwide. Med-rivers are hotspots for biodiversity in all med-regions. Species in med-rivers require different, often opposing adaptive mechanisms to survive drought and flood conditions or recover from them. Thus, metacommunities undergo seasonal differences, reflecting cycles of river fragmentation and connectivity, which also affect ecosystem functioning. River conservation and management is challenging, and trade-offs between environmental and human uses are complex, especially under future climate change scenarios. This overview of a Special Issue on med-rivers synthesizes information presented in 21 articles covering the five med-regions worldwide: Mediterranean Basin, coastal California, central Chile, Cape region of South Africa, and southwest and southern Australia. Research programs to increase basic knowledge in less-developed med-regions should be prioritized to achieve increased abilities to better manage med-rivers.     

Extreme weather events threaten biodiversity and functions of river ecosystems: evidence from a meta-analysis

Both gradual and extreme weather changes trigger complex ecological responses in river ecosystems. It is still unclear to what extent trend or event effects alter biodiversity and functioning in river ecosystems, adding considerable uncertainty to predictions of their future dynamics. Using a comprehensive database of 71 published studies, we show that event – but not trend – effects associated with extreme changes in water flow and temperature substantially reduce species richness. Furthermore, event effects – particularly those affecting hydrological dynamics – on biodiversity and primary productivity were twice as high as impacts due to gradual changes. The synthesis of the available evidence reveals that event effects induce regime shifts in river ecosystems, particularly affecting organisms such as invertebrates. Among extreme weather events, dryness associated with flow interruption caused the largest effects on biota and ecosystem functions in rivers. Effects on ecosystem functions (primary production, organic matter decomposition and respiration) were asymmetric, with only primary production exhibiting a negative response to extreme weather events. Our meta-analysis highlights the disproportionate impact of event effects on river biodiversity and ecosystem functions, with implications for the long-term conservation and management of river ecosystems. However, few studies were available from tropical areas, and our conclusions therefore remain largely limited to temperate river systems. Further efforts need to be directed to assemble evidence of extreme events on river biodiversity and functioning.     

Diverse invertebrate fauna using dry sediment as a refuge in semi-arid and temperate Australian rivers

Dormant aquatic invertebrates can remain viable in riverbed sediment during dry phases, forming a source for recolonisation during wet periods. Regional differences in capacity for invertebrates to survive drying in this way are poorly understood, but may indicate regional differences in vulnerability to altered flow regimes. We compared diversity of invertebrates in dry sediment from intermittent rivers in temperate and semi-arid Australia after 4–8 weeks of drying. We predicted adaptations of semi-arid biota to severe and unpredictable drying would make dry sediment a more significant recolonisation source, with higher relative diversity when compared with temperate rivers. Emerging aquatic invertebrate assemblages were compared to those sampled in nearby pools, as a common drying refuge. Relative taxa richness in rehydrated sediments was higher in the semi-arid region (83 ± 16% of pool taxa) than the temperate (47 ± 6% of pool taxa), despite lower overall richness (24 taxa in semi-arid, 32 taxa in temperate). Semi-arid rivers had greater potential for dry riverbeds to act as a source for recolonisation, given high relative diversity and abundance in dry sediment, combined with the frequent absence of alternative refuges. However, dry riverbeds in both regions provided a significant short-term refuge for aquatic invertebrates.     

Structural and functional responses of invertebrate communities to climate change and flow regulation in alpine catchments

Understanding and predicting how biological communities respond to climate change is critical for assessing biodiversity vulnerability and guiding conservation efforts. Glacier‐ and snow‐fed rivers are one of the most sensitive ecosystems to climate change, and can provide early warning of wider‐scale changes. These rivers are frequently used for hydropower production but there is minimal understanding of how biological communities are influenced by climate change in a context of flow regulation. This study sheds light on this issue by disentangling structural (water temperature preference, taxonomic composition, alpha, beta and gamma diversities) and functional (functional traits, diversity, richness, evenness, dispersion and redundancy) effects of climate change in interaction with flow regulation in the Alps. For this, we compared environmental and aquatic invertebrate data collected in the 1970s and 2010s in regulated and unregulated alpine catchments. We hypothesized a replacement of cold‐adapted species by warming‐tolerant ones, high temporal and spatial turnover in taxa and trait composition, along with reduced taxonomic and functional diversities in consequence of climate change. We expected communities in regulated rivers to respond more drastically due to additive or synergistic effects between flow regulation and climate change. We found divergent structural but convergent functional responses between free‐flowing and regulated catchments. Although cold‐adapted taxa decreased in both of them, greater colonization and spread of thermophilic species was found in the free‐flowing one, resulting in higher spatial and temporal turnover. Since the 1970s, taxonomic diversity increased in the free flowing but decreased in the regulated catchment due to biotic homogenization. Colonization by taxa with new functional strategies (i.e. multivoltine taxa with small body size, resistance forms, aerial dispersion and reproduction by clutches) increased functional diversity but decreased functional redundancy through time. These functional changes could jeopardize the ability of aquatic communities facing intensification of ongoing climate change or new anthropogenic disturbances.     

Influence of damming on anuran species richness in riparian areas: A test of the serial discontinuity concept

Almost all large rivers worldwide are fragmented by dams, and their impacts have been modeled using the serial discontinuity concept (SDC), a series of predictions regarding responses of key biotic and abiotic variables. We evaluated the effects of damming on anuran communities along a 245‐km river corridor by conducting repeated, time‐constrained anuran calling surveys at 42 locations along the Broad and Pacolet Rivers in South Carolina, USA. Using a hierarchical Bayesian analysis, we test the biodiversity prediction of the SDC (modified for floodplain rivers) by evaluating anuran occupancy and species diversity relative to dams and degree of urbanized land use. The mean response of the anuran community indicated that occupancy and species richness were maximized when sites were farther downstream from dams. Sites at the farthest distances downstream of dams (47.5 km) had an estimated ~3 more species than those just below dams. Similarly, species‐specific occupancy estimates showed a trend of higher occupancy downstream from dams. Therefore, using empirical estimation within the context of a 245‐km river riparian landscape, our study supports SDC predictions for a meandering river. We demonstrate that with increasing distance downstream from dams, riparian anuran communities have higher species richness. Reduced species richness immediately downstream of dams is likely driven by alterations in flow regime that reduce or eliminate flows which sustain riparian wetlands that serve as anuran breeding habitat. Therefore, to maintain anuran biodiversity, we suggest that flow regulation should be managed to ensure water releases inundate riparian wetlands during amphibian breeding seasons and aseasonal releases, which can displace adults, larvae, and eggs, are avoided. These outcomes could be achieved by emulating pre‐dam seasonal discharge data, mirroring discharge of an undammed tributary within the focal watershed, or by basing real‐time flow releases on current environmental conditions.     

Biodiversity: towards a unifying theme for river ecology

1. A broadened concept of biodiversity, encompassing spatio‐temporal heterogeneity, functional processes and species diversity, could provide a unifying theme for river ecology. 2. The theoretical foundations of stream ecology often do not reflect fully the crucial roles of spatial complexity and fluvial dynamics in natural river ecosystems, which has hindered conceptual advances and the effectiveness of efforts at conservation and restoration. 3. Inclusion of surface waters (lotic and lentic), subsurface waters (hyporheic and phreatic), riparian systems (in both constrained and floodplain reaches), and the ecotones between them (e.g. springs) as interacting components contributing to total biodiversity, is crucial for developing a holistic framework of rivers as ecosystems. 4. Measures of species diversity, including alpha, beta and gamma diversity, are a result of disturbance history, resource partitioning, habitat fragmentation and successional phenomena across the riverine landscape. A hierarchical approach to diversity in natural and altered river‐floodplain ecosystems will enhance understanding of ecological phenomena operating at different scales along multidimensional environmental gradients. 5. Re‐establishing functional diversity (e.g. hydrologic and successional processes) across the active corridor could serve as the focus of river conservation initiatives. Once functional processes have been reconstituted, habitat heterogeneity will increase, followed by corresponding increases in species diversity of aquatic and riparian biota.     

Benthic and hyporheic invertebrate assemblages along a flow intermittence gradient: effects of duration of dry events

1. A large proportion of the total river length on Earth comprises rivers that are temporary in nature. However, the effects of periodical dry events have received far less attention from ecologists than those of floods and low flows. 2. This study concomitantly examined the effects of flow intermittence on invertebrates from the streambed surface and from a depth of 30 cm in the hyporheic zone. Invertebrates were collected during 3 years in the Albarine River, France, before and after summer dry events from 18 sites (seven were perennial) distributed along a longitudinal flow intermittence gradient. 3. I predicted benthic and hyporheic density and taxonomic richness to decrease, and assemblage composition to shift from desiccation‐sensitive to desiccation‐resistant taxa with increased dry event duration. Second, I predicted benthic and hyporheic assemblages from sites that dried for longer periods to be nested subsets of assemblages from sites that dried for shorter periods. Last, I predicted a convergence in benthic and hyporheic assemblage composition with increasing duration of dry events, resulting from increased vertical migration of benthic taxa into the hyporheic sediments to cope with dry events. 4. Increased dry event duration in the Albarine River led to a decrease in both benthic and hyporheic density and taxonomic richness. Invertebrate assemblage composition shifted along the gradient of increasing flow intermittence, but broad taxonomic overlap between perennial and temporary reaches and nestedness patterns indicated that these shifts were because of the loss of taxa susceptible to drying rather than selection for desiccation‐resistant specialists. 5. Assemblage composition between benthic and hyporheic invertebrates diverged with increasing dry event duration, suggesting that the hyporheic zone did not act as a refuge during dry events in this river. 6. Quantitative studies on the relationships between ecology and intermittence are still rare but are needed to predict the consequences of future changes in flow intermittence. The relationships found in this study should be tested across a wide range of temporary rivers to better evaluate the generality of these findings.     

Implications of climate change for potamodromous fishes

There is little understanding of how climate change will impact potamodromous freshwater fishes. Since the mid 1970s, a decline in annual rainfall in south‐western Australia (a globally recognized biodiversity hotspot) has resulted in the rivers of the region undergoing severe reductions in surface flows (ca. 50%). There is universal agreement amongst Global Climate Models that rainfall will continue to decline in this region. Limited data are available on the movement patterns of the endemic freshwater fishes of south‐western Australia or on the relationship between their life histories and hydrology. We used this region as a model to determine how dramatic hydrological change may impact potamodromous freshwater fishes. Migration patterns of fishes in the largest river in south‐western Australia were quantified over a 4 year period and were related to a number of key environmental variables including discharge, temperature, pH, conductivity and dissolved oxygen. Most of the endemic freshwater fishes were potamodromous, displaying lateral seasonal spawning migrations from the main channel into tributaries, and there were significant temporal differences in movement patterns between species. Using a model averaging approach, amount of discharge was clearly the best predictor of upstream and downstream movement for most species. Given past and projected reductions in surface flow and groundwater, the findings have major implications for future recruitment rates and population viabilities of potamodromous fishes. Freshwater ecosystems in drying climatic regions can only be managed effectively if such hydro‐ecological relationships are considered. Proactive management and addressing existing anthropogenic stressors on aquatic ecosystems associated with the development of surface and groundwater resources and land use is required to increase the resistance and resilience of potamodromous fishes to ongoing flow reductions.     

Habitat dynamics,marine reserve status,and the decline and recovery of coral reef fish communities

Severe climatic disturbance events often have major impacts on coral reef communities, generating cycles of decline and recovery, and in some extreme cases, community‐level phase shifts from coral‐ to algal‐dominated states. Benthic habitat changes directly affect reef fish communities, with low coral cover usually associated with low fish diversity and abundance. No‐take marine reserves (NTRs) are widely advocated for conserving biodiversity and enhancing the sustainability of exploited fish populations. Numerous studies have documented positive ecological and socio‐economic benefits of NTRs; however, the ability of NTRs to ameliorate the effects of acute disturbances on coral reefs has seldom been investigated. Here, we test these factors by tracking the dynamics of benthic and fish communities, including the important fishery species, coral trout (Plectropomus spp.), over 8 years in both NTRs and fished areas in the Keppel Island group, Great Barrier Reef, Australia. Two major disturbances impacted the reefs during the monitoring period, a coral bleaching event in 2006 and a freshwater flood plume in 2011. Both disturbances generated significant declines in coral cover and habitat complexity, with subsequent declines in fish abundance and diversity, and pronounced shifts in fish assemblage structure. Coral trout density also declined in response to the loss of live coral, however, the approximately 2:1 density ratio between NTRs and fished zones was maintained over time. The only post‐disturbance refuges for coral trout spawning stocks were within the NTRs that escaped the worst effects of the disturbances. Although NTRs had little discernible effect on the temporal dynamics of benthic or fish communities, it was evident that the post‐disturbance refuges for coral trout spawning stocks within some NTRs may be critically important to regional‐scale population persistence and recovery.     

An unexpected source of invertebrate community recovery in intermittent streams from a humid continental climate

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The invertebrate fauna of a physically modified urban river

The typical urban river is affected by various factors relating to water quality problems, physical habitat modification (for flood prevention) and flashy flows. These restrict macroinvertebrate biodiversity such that a few tolerant taxa may dominate and more sensitive organisms may be completely absent. This paper presents the findings of a year long, macroinvertebrate survey of an urban river catchment and investigates the effects of physical habitat modification on macroinvertebrates using various analytical tools. It is demonstrated that considerable variation in invertebrate species, abundance, diversity and tolerance exists between different urban rivers, sites on the same river and individual sites at different sampling times. Analysis of paired sites with similar water quality, but contrasting physical habitat, indicates that less modified sites support a slightly higher quality macroinvertebrate fauna (defined by biotic score and beta diversity) than heavily engineered sites. It is concluded that water quality is the primary limiting factor of invertebrate biodiversity in the heavily urbanized River Tame catchment. The removal of heavy engineering structures may facilitate improvements to invertebrate fauna in urban rivers only in conjunction with improvements to water quality.     

Parallels and contrasts between intermittently freezing and drying streams: From individual adaptations to biodiversity variation

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雅鲁藏布江流域底栖动物多样性及生态评价

雅鲁藏布江起源于喜马拉雅山,是世界上海拔最高的河流之一,是流经我国西藏境内重要的国际河流,其河流生态系统具有特殊地貌及生态条件。研究该流域底栖动物多样性分布特征及其影响因子,是科学评价该区域河流生态系统健康状况,实现资源可持续开发利用的基础。2009年10月—2010年6月期间,以底栖动物作为指示物种,对雅江流域干支流及堰塞湖的14个采样断面进行河流生态评价。采用Alpha及Beta生物多样性指数分别指示局部采样河段及全区域的底栖动物多样性。对采样断面底栖动物组成分析发现:14个采样断面共采集到底栖动物110种,隶属57科102属。雅江干流底栖动物种类数最高为29,平均为19。支流年楚河种类数为17。支流拉萨河,尼洋河,帕龙藏布的最高种类数分别为25,33,36;平均种类数分别为21,21,22,生物多样性普遍高于干流。整个流域中底栖动物平均种类数相差不大,但种类组成和密度相差较大。调查区域的Beta多样性指数β高于低海拔地区的相似的山区河流,说明雅江流域内底栖动物群落差异性高于正常海拔地区。对14个采样断面的物种组成进行除趋势对应分析表明:影响雅江流域底栖动物多样性的主要因素为河型,河床阻力结构,堤岸结构,水流流速。保持稳定的阶梯-深潭结构和自然堤岸结构,以及适宜的流速有利于保护雅江河流生态。     

Hyporheic invertebrates as bioindicators of ecological health in temporary rivers: A meta-analysis

Worldwide, many rivers cease flow and dry either naturally or owing to human activities such as water extraction. However, even when surface water is absent, diverse assemblages of aquatic invertebrates inhabit the saturated sediments below the river bed (hyporheic zone). In the absence of surface water or flow, biota of this zone may be sampled as an alternative to surface water-based ecological assessments. The potential of hyporheic invertebrates as ecological indicators of river health, however, is largely unexplored. We analysed hyporheic taxa lists from the international literature on temporary rivers to assess compositional similarity among broad-scale regions and sampling conditions, including the presence or absence of surface waters and flow, and the regional effect of hydrological phase (dry channel, non-flowing waters, surface flow) on richness. We hypothesised that if consistent patterns were found, then effects of human disturbances in temporary rivers may be assessable using hyporheic bioindicators. Assemblages differed geographically and by climate, but hydrological phase did not have a strong effect at the global scale. However, hyporheic assemblage composition within regions varied along a gradient of higher richness during wetter phases. This indicates that within geographic regions, hyporheic responses to surface drying are predictable and, by extension, hyporheic invertebrates are potentially useful ecological indicators of temporary river health. With many rivers now experiencing, or predicted to experience, lower flows and longer dry phases owing to climate change, the development of ecological assessment methods specific to flow intermittency is a priority. We advocate expanded monitoring of hyporheic zones in temporary rivers and recommend hyporheic invertebrates as potential bioindicators to complement surface water assessments.     

Anthropogenic disturbance homogenizes seagrass fish communities

Anthropogenic activities have led to the biotic homogenization of many ecological communities, yet in coastal systems this phenomenon remains understudied. In particular, activities that locally affect marine habitat‐forming foundation species may perturb habitat and promote species with generalist, opportunistic traits, in turn affecting spatial patterns of biodiversity. Here, we quantified fish diversity in seagrass communities across 89 sites spanning 6° latitude along the Pacific coast of Canada, to test the hypothesis that anthropogenic disturbances homogenize (i.e., lower beta‐diversity) assemblages within coastal ecosystems. We test for patterns of biotic homogenization at sites within different anthropogenic disturbance categories (low, medium, and high) at two spatial scales (within and across regions) using both abundance‐ and incidence‐based beta‐diversity metrics. Our models provide clear evidence that fish communities in high anthropogenic disturbance seagrass areas are homogenized relative to those in low disturbance areas. These results were consistent across within‐region comparisons using abundance‐ and incidence‐based measures of beta‐diversity, and in across‐region comparisons using incidence‐based measures. Physical and biotic characteristics of seagrass meadows also influenced fish beta‐diversity. Biotic habitat characteristics including seagrass biomass and shoot density were more differentiated among high disturbance sites, potentially indicative of a perturbed environment. Indicator species and trait analyses revealed fishes associated with low disturbance sites had characteristics including stenotopy, lower swimming ability, and egg guarding behavior. Our study is the first to show biotic homogenization of fishes across seagrass meadows within areas of relatively high human impact. These results support the importance of targeting conservation efforts in low anthropogenic disturbance areas across land‐ and seascapes, as well as managing anthropogenic impacts in high activity areas.