Effects of flooding on recruitment and dispersal of the Southern Pygmy Perch (Nannoperca australis) at a Murray River floodplain wetland

Summary With limited evidence linking Australia's Murray‐Darling Basin fish species and flooding, this study assessed annual variation in abundance and recruitment levels of a small‐bodied, threatened floodplain species, the Southern Pygmy Perch (Nannoperca australis), in floodplain habitats (creeks, lakes and wetlands) in the Barmah‐Millewa Forest, Murray River, Australia. Spring and summer sampling over a 5‐year period encompassed large hydrological variation, including 1 year of extended floodplain inundation which was largely driven by an environmental water release, and 2 years of severe regional drought. Recruitment and dispersal of Southern Pygmy Perch significantly increased during the floodplain inundation event compared with the other examined years. This study provides valuable support for an environmental water allocation benefiting a native species, and explores the link between flooding and its advantages to native fish. This suggests that the reduced flooding frequency and magnitude as a result of river regulation may well be a major contributing factor in the species’ decline in the Murray‐Darling Basin.     

Floodplain ants show a stronger response to an extensive flood than to variations in fallen‐timber load

Understanding how species respond to differences in resource availability is critical to managing biodiversity under the increasing pressures associated with climate change and growing human populations. Over the last century, the floodplain forests of Australia's largest river system, the Murray‐Darling Basin, have been much affected by intensive harvesting of timber and firewood, and increasingly stressed by river regulation and, recently, an extended drought. Fallen timber – logs and shed branches – is known to play a key role in the ecology of several important species on these floodplains. Here, we monitored the response of the ant assemblages of a floodplain forest along the Murray River to a large‐scale (34 ha) experimental manipulation of fallen‐timber load (0 to 80 t ha^?1) over 4 years. The forest was subjected to an incidental, extensive flood that enabled us to examine how two important stressors (timber removal and river regulation) affect ant assemblages. Ants showed little response to the proximity of fallen timber within plots, prior to the flood, or to different loads among plots, unlike other floodplain biota. After the flood, both ant abundance and species richness increased and species composition changed. However, this increase in species richness after flooding was less pronounced in plots with higher amounts of fallen timber. Managing river red gum forest using a mosaic of flood regimes, more representative of historical conditions, is likely to be the most effective way to maintain and enhance the diversity of ants and other biota on these important floodplains.     

Characterisation of Adaptive Genetic Diversity in Environmentally Contrasted Populations of Eucalyptus camaldulensis Dehnh. (River Red Gum)

As an increasing number of ecosystems face departures from long standing environmental conditions under climate change, our understanding of the capacity of species to adapt will become important for directing conservation and management of biodiversity. Insights into the potential for genetic adaptation might be gained by assessing genomic signatures of adaptation to historic or prevailing environmental conditions. The river red gum (Eucalyptus camaldulensis Dehnh.) is a widespread Australian eucalypt inhabiting riverine and floodplain habitats which spans strong environmental gradients. We investigated the effects of adaptation to environment on population level genetic diversity of E. camaldulensis, examining SNP variation in candidate gene loci sampled across 20 climatically diverse populations approximating the species natural distribution. Genetic differentiation among populations was high (F_ST = 17%), exceeding previous estimates based on neutral markers. Complementary statistical approaches identified 6 SNP loci in four genes (COMT, Dehydrin, ERECTA and PIP2) which, after accounting for demographic effects, exhibited higher than expected levels of genetic differentiation among populations and whose allelic variation was associated with local environment. While this study employs but a small proportion of available diversity in the eucalyptus genome, it draws our attention to the potential for application of wide spread eucalypt species to test adaptive hypotheses.     

Ecological impacts of dams,water diversions and river management on floodplain wetlands in Australia

Australian floodplain wetlands are sites of high biodiversity that depend on flows from rivers. Dams, diversions and river management have reduced flooding to these wetlands, altering their ecology, and causing the death or poor health of aquatic biota. Four floodplain wetlands (Barmah‐Millewa Forest and Moira Marshes, Chowilla floodplain, Macquarie Marshes, Gwydir wetlands) illustrate these effects with successional changes in aquatic vegetation, reduced vegetation health, declining numbers of water‐birds and nesting, and declining native fish and invertebrate populations. These effects are likely to be widespread as Australia has at least 446 large dams (>10 m crest height) storing 8.8 × 10⁷ ML (10⁶ L) of water, much of which is diverted upstream of floodplain wetlands. More than 50% of floodplain wetlands on developed rivers may no longer flood. Of all of the river basins in Australia, the Murray‐Darling Basin is most affected with dams which can store 103% of annual runoff and 87% of divertible water extracted (1983–84 data). Some floodplain wetlands are now permanent storages. This has changed their biota from one tolerant of a variable flooding regime, to one that withstands permanent flooding. Plans exist to build dams to divert water from many rivers, mainly for irrigation. These plans seldom adequately model subsequent ecological and hydrological impacts to floodplain wetlands. To avoid further loss of wetlands, an improved understanding of the interaction between river flows and floodplain ecology, and investigations into ecological impacts of management practices, is essential.     

Tree health and regeneration response of Black Box (Eucalyptus largiflorens) to recent flooding

Black Box (Eucalyptus largiflorens) is a dominant floodplain tree in the Murray–Darling Basin. In northern Victoria, the health of Black Box woodlands has declined as a consequence of river regulation and drought. This has raised concern about the long‐term survival of populations. Although tree health and regeneration of this species are entwined with flooding, there is limited knowledge of its response to environmental watering. This inhibits the effective implementation of management actions to secure the long‐term survival of floodplain Black Box populations. We investigated the effect of flooding history on Black Box tree health, population status and regeneration at 26 sites within the Murray Sunset National Park, Victoria. Sites were assessed under two flooding treatments: (1) ‘recently flooded’ (sites frequently flooded within the last 5 years and (2) ‘historically flooded’ (sites not flooded since 1993). Black Box populations in recently flooded sites had a greater range of life stages present and fewer dead trees, indicating a healthier and more sustainable population structure. In addition, trees were in better health with higher canopy condition and reproductive output (e.g. flowers and fruits), and the average tree diameter was greater than in historically flooded sites. Seedlings and saplings were present only at recently flooded sites, indicating that water availability and tree health are a strong determinant of regeneration in these landscapes. Flooding is an important factor in the sustainability of Black Box populations in this Victorian semi‐arid floodplain. A key recommendation is that managed flows should be implemented to target populations in poor condition. Although regular flooding is required to maintain or improve the health of Black Box populations, developing the optimum flow regime (timing, frequency and duration) to facilitate this outcome requires further investigation.     

Current Loads of Coarse Woody Debris on Southeastern Australian Floodplains: Evaluation of Change and Implications for Restoration

We evaluated the status of coarse woody debris (CWD, fallen wood) on floodplains of the southern Murray‐Darling basin of southeastern Australia. The floodplains are dominated floristically by the river red gum Eucalyptus camaldulensis. Aerial survey techniques were used to estimate the amounts of woody debris within 200 m of the channels along 2,442 km of 11 rivers of the system, including the Murray and Darling Rivers and the Darling Anabranch. Aerially based indices were converted into wood volumes by using ground‐truthing at a selection of sites; there was a strong correlation between index values and measured wood volume densities. For thickly forested sites such as Barmah, Gunbower Island, and the Ovens floodplains, the aerial method was not useful, so ground measurements at randomly positioned sites within the forests were used. Volumes were translated into mass by using conversion factors drawn from the literature. We estimated that total tonnage on approximately 221,000 ha of floodplain forests was 4.175 ± 0.579 × 10⁶ tonne. In the larger forested blocks (>7,000 ha), mean wood densities ranged between approximately 12 tonne/ha on the lower Goulburn up to approximately 24 tonne/ha at Barmah State Forest. The area‐weighted mean for the entire area was approximately 19 tonne/ha. A main purpose of the research was to place these figures into an historical perspective to evaluate implications for restoration. A thorough search of historical documentation revealed that there are no extant data upon which to estimate pre‐European settlement levels. We used information from an apparently undisturbed “unmanaged” site in the Millewa forests of southern New South Wales as a basis. Wood density there corresponded to a mean figure of 125 tonne/ha wood‐mass density. By using this figure we estimate that CWD levels on the southern Murray‐Darling basin may be of the order of 15% of pre‐European settlement levels. Full restoration of the 221,000 ha surveyed would require 23.5 ± 0.579 × 10⁶ tonne, which is equivalent to about 600,000 mature (1 m diameter at breast height) river red gum trees or the amount of timber derived from clear felling about 115,000 ha of river red gum forest at current stocking levels. We discuss the implications of this massive deficit and possible short‐ and long‐term solutions.     

Spangled perch (Leiopotherapon unicolor) in the southern Murray‐Darling Basin: Flood dispersal and short‐term persistence outside its core range

The spangled perch Leiopotherapon unicolor is considered a rare vagrant in the southern Murray‐Darling Basin, Australia, due to its intolerance of the relatively cool water temperatures that prevail during winter months. This study details 1342 records of the species from 68 locations between 2010 and 2014 outside its accepted ‘core adult range’ following widespread flooding during 2010 and 2011. Although records of the species declined over 2013, L. unicolor remained resident in the southern Murray‐Darling Basin as of April 2014. The species persisted in several locations for three consecutive winters with recruitment documented at two sites. This study represents the first identification of the dispersal of large numbers of L. unicolor into the southern Murray‐Darling Basin, persistence beyond a single winter, and recruitment by the species in habitats south of its recognized ‘core adult range’. Targeted research would determine the potential for predicted environmental changes (artificially warmer drainage wetlands, climate change and greater floodplain connectivity) to facilitate longer term persistence and range expansion by the species in the southern Murray‐Darling Basin.     

The influence of leaf litter on zooplankton in floodplain wetlands: changes resulting from river regulation

1. The loss of input of leaf litter through clearing of riparian vegetation may result in significant changes to aquatic ecosystems. River red gums (Eucalyptus camaldulensis) surrounding floodplain wetlands in the Murray–Darling Basin, Australia, contribute large quantities of leaf litter, but the quality of this resource may change depending on the timing of inundation. 2. We used experimental mesocosms to test the hypotheses that zooplankton would have a greater abundance with an input of leaf litter and that fewer zooplankton would emerge from egg banks in cleared than forested wetlands. The experiment was carried out in summer/autumn and in spring to test a third hypothesis that zooplankton would respond to changes in the timing of wetland inundation as a result of river regulation. 3. In summer/autumn, leaf litter reduced zooplankton abundance by 89% at the beginning of the experiment through its influence on water quality. Only a few taxa (Polyarthra spp., Colurella spp. and the cladoceran Family Moinidae) responded positively to leaf litter when water quality improved later in the experiment, indicating a switch in the role of leaf litter from a non‐trophic to a trophic pathway. 4. In spring, microcrustaceans emerged in smaller numbers from sediment sourced from cleared compared to forested wetlands, reflecting different communities in these two wetland types and/or disturbances to the sediment that interfere with emergence. 5. Although leaf litter appears not to be an important resource for zooplankton in floodplain wetlands, riparian clearing may have lasting effects on future emerging zooplankton communities. Additionally, river regulation may have considerable impacts on the influence of leaf litter on zooplankton, which has implications for the management of floodplain river systems.     

Immediate and longer-term effects of managed flooding on floodplain invertebrate assemblages in south-eastern Australia: generation and maintenance of a mosaic landscape

1. We compared assemblages of ground‐active, terrestrial beetles and spiders from different areas of river red gum Eucalyptus camaldulensis floodplain forest in subhumid, south‐eastern Australia before and for 2 years following a managed flood to determine whether the Flood Pulse Concept is an appropriate ecological model for this regulated, lowland river‐floodplain system. 2. Immediately following flooding, the abundance, species richness and biomass of beetles were greatest at sites that had been inundated for the longest period (approximately 4 months). The abundance, species richness and biomass of spiders were not reduced at sites that were flooded for 4 months compared with unflooded or briefly flooded areas. Sites recently flooded for several months had high densities of predatory, hygrophilic beetles (Carabidae) and spiders (Lycosidae). 3. Over the 2 years following the flood, beetles generally were more abundant at sites that had been inundated for longer. At all sampling times, the species richness of beetles at sites increased with the length of time sites were inundated, even before the flood. Neither the abundance nor species richness of spiders was related to duration of flooding. 4. The structure of beetle and spider assemblages at sites that were flooded for different lengths of time did not appear to converge monotonically over the 2 years after the flood. 5. Managed flooding promotes diversity of beetles and spiders both by providing conditions that create a ‘pulse’ in populations of hygrophilic specialists in the short term, and by creating subtle, persistent changes in forest‐floor conditions. Despite its monotypic canopy, river red gum floodplain forest is a habitat mosaic generated by differing inundation histories.     

Hypoxic blackwater event severely impacts Murray crayfish (Euastacus armatus) populations in the Murray River,Australia

Prolonged flooding in 2010/11 ended a decade of drought and produced a large‐scale hypoxic blackwater event across the southern Murray‐Darling Basin, Australia. The hypoxic conditions caused fish kills and Murray crayfish Euastacus armatus to emerge from the water onto the river banks to avoid the poor water quality. This study examined the medium‐term impact of this blackwater event on Murray crayfish populations in the Murray River, where approximately 1800 km of the main channel were affected by hypoxia. Murray crayfish populations were surveyed in July 2012, along a 1100‐km section of the Murray River at 10 sites affected by hypoxic blackwater and six sites that were not affected, and data were compared with surveys of the same sites undertaken in July 2010, four months before the hypoxic blackwater event (before‐after‐control‐impact experimental design). Murray crayfish abundance in 2012 (post‐blackwater) was significantly lower at blackwater affected sites (81% reduction from 2010), but not at non‐affected sites. The hypoxic blackwater impacted Murray crayfish of both sexes and all size‐classes in a similar manner. The results demonstrate that prolonged periods of hypoxia can markedly impact populations of the long‐lived and slow‐growing Murray crayfish despite the species ability to emerge from hypoxic water. The findings highlight important challenges for the management of both the recreational fishery for this species and riverine flows in relation to hypoxic blackwater events.     

Zooplankton response to flooding of a drought refuge and implications for the endangered fish species Craterocephalus fluviatilis cohabiting with alien Gambusia holbrooki

Disruption to a river’s natural flow regime changes its ecological character, which becomes unfavourable for previously adapted biota. The zooplankton particularly are affected, and survival of larval and juvenile fish is largely determined by their availability. Alien fishes can also impact on recruitment in native fishes, sometimes through competition. In this regard, the invasive eastern Gambusia Gambusia holbrooki is linked to the decline of several fish species. It can have a substantial influence in shaping plankton communities, which implies that it competes with native fish that rely on the microfauna. The effects of river regulation and over abstraction of water in the Murray–Darling Basin, south-eastern Australia, were exacerbated by drought from 1997 to 2010. Consequently, the endangered Murray hardyhead Craterocephalus fluviatilis underwent substantial population decline and extirpations. The purpose of this study is to determine if a link exists between zooplankton response to flooding of a drought refuge and the recruitment success of C. fluviatilis in the presence of G. holbrooki. Flooding triggered sharp and substantial increases in the zooplankton and their eggs, which was the sole food of C. fluviatilis. This apparently benefitted the recruitment of C. fluviatilis, and sometimes alleviated diet overlap with G. holbrooki. Conversely, the zooplankton in a nearby non-flooded refuge was low in abundance and diversity, and all fish species were extirpated. The findings indicate that the flooding of drought refugia with relatively small volumes of water can be timed with ecological cues that would otherwise be desynchronized in highly regulated rivers, particularly during drought.     

River Red Gum (Eucalyptus camaldulensis Dehnh.) organic matter as a carbon source in the lower Darling River,Australia

The Darling River, in New South Wales, Australia, is a large semi-arid system with a highly variable flow regime, characterised by unpredictable events of flooding and drought. In large lowland rivers like the Darling, lateral (river-floodplain) interactions can greatly influence both physical and biological components of the system. The floodplain and riparian zone of the Darling River is dominated by River Red Gum (RRG), Eucalyptus camaldulensis. The large amount of organic matter they produce accumulates on the floodplain and on benches within the channel, and is subject to alternate periods of flooding and drying as a result of highly variable flows. This paper examines the effect of alternate periods of flooding and drying on the processing of E. camaldulensis organic matter. Results of the 6-month in situ field study, together with results from laboratory experiments comparing dissolved organic carbon (DOC) release from various RRG litter types, suggest that RRG leaves provide the most bio-available source of carbon to the system, while bark may be more important as a habitat for invertebrates and other fauna. Laboratory experiments exploring the effect of drying and re-flooding on litter breakdown and release of DOC suggested that the majority of DOC was released from RRG leaves in the first 24 h of inundation. Also, upon drying and re-flooding of the leaves, a smaller but significant release of DOC occurred. However, an alternative wet/dry cycle did not affect weight loss of the leaf litter. Results of the field and lab experiments suggest that RRG leaves represent an important source of carbon to the Darling River, with inputs being influenced by the highly variable flow regime.     

Effects of flooding on recruitment and abundance of Golden Perch (Macquaria ambigua ambigua) in the lower River Murray

Flooding is often considered a stimulus for production of fish in floodplain rivers. In the southern Murray–Darling Basin (MDB), Australia, however, few native fish species have been shown to use the floodplain for spawning, and recruitment has been positively and negatively associated with flooding. In 2010/11, extensive flooding in the lower River Murray provided an opportunity to investigate the recruitment response of Golden Perch (Macquaria ambigua ambigua) following 10 years of drought and floodplain isolation. Annual variation in Golden Perch abundance and recruitment were investigated in anabranch and main channel habitats at Chowilla in the floodplain geomorphic region of the lower River Murray over a 7‐year period incorporating the flood and 6 years of in‐channel flow. Spatial variation in recruitment in the lower River Murray was also investigated by comparing the age structure of Golden Perch in the swamplands/lakes, gorge and floodplain geomorphic regions. Golden Perch abundance in the Chowilla region increased significantly postflooding compared with drought years. Age structures indicated that increased abundance was due predominantly to fish spawned during the flood (2010/11) and the previous year (2009/10), which was characterised by in‐channel flows. Age structure was similar in the nearby Katarapko Anabranch system indicating a uniform postflood recruitment response in the floodplain geomorphic region. Juvenile Golden Perch from the 2010/11 and 2009/10 cohorts were less apparent in the gorge and swamplands/lakes regions. Golden Perch have flexible life histories and will spawn and recruit in association with in‐channel rises in flow and overbank flows, but significant increases in abundance in the lower River Murray may result from overbank flooding. Contemporary approaches to flow restoration in the MDB emphasise overbank flows and floodplain processes. We suggest, however, that environmental flow management that incorporates floodplain and in‐channel processes, at appropriate spatio‐temporal scales, will result in more robust populations of Golden Perch.     

Continental impacts of water development on waterbirds,contrasting two Australian river basins: Global implications for sustainable water use

The world's freshwater biotas are declining in diversity, range and abundance, more than in other realms, with human appropriation of water. Despite considerable data on the distribution of dams and their hydrological effects on river systems, there are few expansive and long analyses of impacts on freshwater biota. We investigated trends in waterbird communities over 32 years, (1983–2014), at three spatial scales in two similarly sized large river basins, with contrasting levels of water resource development, representing almost a third (29%) of Australia: the Murray–Darling Basin and the Lake Eyre Basin. The Murray–Darling Basin is Australia's most developed river basin (240 dams storing 29,893 GL) while the Lake Eyre Basin is one of the less developed basins (1 dam storing 14 GL). We compared the long‐term responses of waterbird communities in the two river basins at river basin, catchment and major wetland scales. Waterbird abundances were strongly related to river flows and rainfall. For the developed Murray–Darling Basin, we identified significant long‐term declines in total abundances, functional response groups (e.g., piscivores) and individual species of waterbird (n = 50), associated with reductions in cumulative annual flow. These trends indicated ecosystem level changes. Contrastingly, we found no evidence of waterbird declines in the undeveloped Lake Eyre Basin. We also modelled the effects of the Australian Government buying up water rights and returning these to the riverine environment, at a substantial cost (>3.1 AUD billion) which were projected to partly (18% improvement) restore waterbird abundances, but projected climate change effects could reduce these benefits considerably to only a 1% or 4% improvement, with respective annual recovery of environmental flows of 2,800 GL or 3,200 GL. Our unique large temporal and spatial scale analyses demonstrated severe long‐term ecological impact of water resource development on prominent freshwater animals, with implications for global management of water resources.     

A conceptual model of tree behaviour improves the visual assessment of tree condition

A conceptual model describing the response of two Australian floodplain eucalypts, river red gum (Eucalyptus camaldulensis) and black box (Eucalyptus largiflorens), to changes in water availability was developed based on field observations. This model was incorporated into a percentage based visual method estimating two tree crown parameters, crown extent and density. Extent is the amount of foliage at the periphery of the assessable crown; density is the density of assessable crown foliage. Polychoric correlation was used to determine the level of agreement between two experienced observers assessing river red gum and black box trees using a simple percentage scale and a percentage scale supported by the conceptual model. Trees were evaluated using the model by determining their position on a trajectory of water stress related decline and response. In both cases observer estimates of crown extent and density were significantly correlated. With the exception of red gum crown density the correlation coefficients were higher for the model supported scale. Using a conceptual model of tree response to water availability improved observer agreement. Supporting subjective assessment systems with a conceptual model is recommended to improve observer agreement in cases where a distinct model of the dominant stressor can be defined.     

A standardised approach to calculating floodplain tree condition to support environmental watering decisions

Ground-based visual assessment of crown condition is a cornerstone of tree condition assessment globally, and numerous condition assessment approaches have evolved to address the needs and perspectives of different users. In Australia’s iconic Murray–Darling Basin (MDB), stands of floodplain eucalypts are increasingly vulnerable to a range of interacting stressors related to climate change and over-extraction of water for consumptive and agricultural use. A standardised approach developed in 2008 for assessing floodplain trees within the MDB provides extensive guidance to ensure field data is collected consistently. However, there is minimal instruction on how to interpret data, and consequently a range of evaluation approaches have evolved. The lack of a standardised reporting framework generated by these different approaches makes it difficult for floodplain managers and environmental water holders to make repeatable, robust decisions for prioritising water allocations across competing locations. To provide improved lines of evidence to support decision making, this paper describes a ‘best-practise’ approach to calculating a tree condition score from field data. Within, we document existing approaches in the southern Murray–Darling Basin, and recommend a method that meets the needs of floodplain managers as a pragmatic reporting, communication and decision support tool that does not require statistical analysis. Case studies and a revised conceptual model of tree decline and recovery are provided to demonstrate the validity of the recommended approach.

     

Phylogeography of the widespread Australian freshwater prawn, Macrobrachium australiense (Decapoda, Palaemonidae)

Aim To investigate the phylogeographic structure of the widespread freshwater prawn, Macrobrachium australiense, within and between major Australian drainage basins using mitochondrial sequence data. This will enable the investigation of historical connections between major drainages and examination of hypotheses of biogeographic associations among Australian freshwater basins. Location Inland, eastern and northern Australia. Methods Sequencing 16S rRNA and ATPase 6 protein coding mitochondrial DNA genes from M. australiense from 19 locations from inland, eastern and northern Australia. Results Within drainage basins, haplotype trees are monophyletic, with the exception of the Finke River from the Lake Eyre Basin. Macrobrachium australiense from the two main inland drainages, the Murray–Darling and Lake Eyre Basin are divergent from each other and do not form a monophyletic group, instead the Murray–Darling Basin haplotypes clade with eastern coastal haplotypes. Haplotypes from neighbouring eastern coastal drainages were found to be quite divergent from each other. Main conclusions The phylogeographic relationships among M. australiense suggest that the two major inland drainages, the Murray–Darling Basin and the Lake Eyre Basin, are not biogeographically closely associated to each other. Instead the Murray–Darling Basin is more closely allied with the eastern coastal drainages across the Great Dividing Range. Despite their proximity the neighbouring southeast Queensland coastal Mary and Brisbane Rivers are also biogeographically divergent from each other. The results also indicate that the Finke River appears to have been isolated from the remainder of the Lake Eyre Basin catchment for a significant period of time.     

On the roles of landscape heterogeneity and environmental variation in determining population genomic structure in a dendritic system

Dispersal and natural selection are key evolutionary processes shaping the distribution of phenotypic and genetic diversity. For species inhabiting complex spatial environments however, it is unclear how the balance between gene flow and selection may be influenced by landscape heterogeneity and environmental variation. Here, we evaluated the effects of dendritic landscape structure and the selective forces of hydroclimatic variation on population genomic parameters for the Murray River rainbowfish, Melanotaenia fluviatilis across the Murray–Darling Basin, Australia. We genotyped 249 rainbowfish at 17,503 high‐quality SNP loci and integrated these with models of network connectivity and high‐resolution environmental data within a riverscape genomics framework. We tested competing models of gene flow before using multivariate genotype–environment association (GEA) analysis to test for signals of adaptive divergence associated with hydroclimatic variation. Patterns of neutral genetic variation were consistent with expectations based on the stream hierarchy model and M. fluviatilis’ moderate dispersal ability. Models incorporating dendritic network structure suggested that landscape heterogeneity is a more important factor determining connectivity and gene flow than waterway distance. Extending these results, we also introduce a novel approach to controlling for the unique effects of dendritic network structure in GEA analyses of populations of aquatic species. We identified 146 candidate loci potentially underlying a polygenic adaptive response to seasonal fluctuations in stream flow and variation in the relative timing of temperature and precipitation extremes. Our findings underscore an emerging predominant role for seasonal variation in hydroclimatic conditions driving local adaptation and are relevant for informing proactive conservation management.