Fish recruitment in rivers with modified discharge depends on the interacting effects of flow and thermal regimes

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Modelling the impacts of flow regulation on fish distributions in naturally intermittent lowland streams: an approach for predicting restoration responses

1. Understanding the relationships between flow regime and the distribution of biota is critical for managing flows in regulated rivers. In northern Victoria, Australia, efforts are presently underway to restore a natural, intermittent flow regime to several streams which, for over 100 years, have received perennial diversions as part of a stock, irrigation and domestic water supply. 2. Bayesian, model‐averaged, binomial regression was used to predict probabilities of occurrence for 13 fish species, including five non‐native species, based on hydrologic variables characterising both the current and modelled future flow regimes at 10 sites representing a range of hydrologic regimes (categorised here as heavily regulated, moderately regulated and unregulated). 3. Regression models accurately predicted present probabilities of occurrence for most species across all sites. The models predicted a reduced likelihood of large, native, flow‐dependent species occurring at regulated sites following flow restoration. Predictions regarding the future distribution of widespread species including two small‐bodied native and four exotic species were less certain as current distributions of these widespread species were unrelated to hydrologic variables we examined and thus unlikely to be significantly affected by flow restoration. The distributions of two small native species currently restricted to unregulated sites are predicted to increase throughout the system. 4. This study illustrates the effects of artificially induced perennial flow on lowland fish distributions. Furthermore, the combination of pre‐restoration data together with predictive modelling provides valuable insights into the likely outcomes of flow regime shifts. 5. This study clearly demonstrates the value of combining empirical research and modelling in guiding environmental flow and ecosystem restoration decisions. Knowledge from the study is now helping guide management decisions and the development of mitigation strategies to protect highly valued species in the system from potential future threats.     

More for less: a study of environmental flows during drought in two Australian rivers

1. In rivers affected by drought, flow regulation can further reduce flow and intensify its effects. We measured ecological responses to environmental flows, during a prolonged drought in a regulated river (Cotter River), compared with a drought affected, unregulated river (Goodradigbee River) in south‐eastern Australia. 2. Environmental flows in the regulated Cotter River were reduced from a monthly average base flow of 15 MLd^?1 to only 5 MLd^?1, which was implemented as two test flow regimes. Initially, flows were delivered in cycles of 14 days at 3 MLd^?1 followed by 3 days at 14 MLd^?1 and then another 14 days at 3 MLd^?1 to make up the monthly average of 5 MLd^?1. This flow regime continued for 6 months, after which a preliminary ecological assessment indicated deterioration in river condition. Consequently, the flow regime was altered to a cycle of 2 MLd^?1 for 28 days followed by 20 MLd^?1 for either 3 or 4 days. This new flow regime continued for another 5 months. 3. The ecological outcomes of the test flow regimes were assessed in terms of (i) the provision of available habitat (wetted channel) for aquatic biota; (ii) the accumulation of periphyton; and (iii) the structure and richness of macroinvertebrate assemblages. 4. Flow of 20 MLd^?1 covered most of the streambed in the Cotter River, thus providing more wetted area and connectivity between habitats than flows of 2, 3 or 14 MLd^?1. Depth and velocity were always less in the Cotter River than in the unregulated Goodradigbee River. Periphyton decreased in the Cotter River during the 2/20 MLd^?1 flow regime, which combined the lowest and greatest test flow volumes, while periphyton did not change significantly in the unregulated river. 5. The reduced flow in the Cotter River resulted in fewer macroinvertebrates than expected (13) compared with unregulated Goodradigbee sites (19), although the magnitude of the differences did not depend on the test flow releases. Macroinvertebrates in the Cotter River became numerically dominated by Diptera and Oligochaeta, while Ephemeroptera, Plecoptera and Trichoptera decreased in abundance. 6. In the Cotter River, the monthly average flow of 5 MLd^?1 (exceeded 97% of the time pre‐regulation) was insufficient to maintain the macroinvertebrate assemblages in reference condition, regardless of release patterns. However, short‐term ecological objectives were achieved, such as reduced periphyton accumulation and increased habitat availability, and the environmental flows maintained the river’s ability to recover (resilience) when higher flows returned.     

Effects of an experimental environmental flow release on the diet of fish in a regulated coastal Australian river

Environmental flow rules are developed to provide a flow regime necessary to maintain healthy river and floodplain ecosystems in rivers regulated for human uses. However, few studies have experimentally assessed potential ecological mechanisms causing declines in the health and productivity of freshwater fish assemblages in regulated rivers to inform the development of appropriate environmental flows. We tested whether an experimental flow release in a regulated tributary of the Hunter River, Australia, altered the diet of two widely distributed fish species (Australian smelt Retropinna semoni and Cox’s gudgeon Gobiomorphus coxii) compared with data from unregulated reference and regulated control tributaries. Neither species had significant differences in the number of prey taxa ingested, gut fullness or composition of gut contents due to the environmental flow release (EFR). The diet of R. semoni did not differ significantly between regulated and unregulated tributaries in either catchment. However, the diet of G. coxii differed in only one of the two pairs of rivers consistently across all sample times. Assuming the EFR was sufficient to alter the composition of prey available for consumption by the fish species studied, our findings imply that functional indicators, such as the diet of generalist higher-order consumers, may be more suitable indicators of long-term flow regime change rather than short-term flow events.     

Flow regulation affects temporal patterns of riverine plant seed dispersal: potential implications for plant recruitment

1. Changes to the natural flow regime of a river caused by flow regulation may affect waterborne seed dispersal (hydrochory), and this may be an important mechanism by which regulation affects riverine plant communities. We assessed the effect of altered timing of seasonal flow peaks on hydrochory and considered the potential implications for plant recruitment. 2. We sampled hydrochory within five lowland rivers of temperate Australia, three of which are regulated by large dams. These dams are operated to store winter and spring rains and release water in summer and autumn for agriculture. At three sites on each river, hydrochory was sampled monthly for 12 months using passive drift nets. The contents of the drift samples were determined using the seedling‐emergence method. 3. More than 33 000 seedlings from 142 taxa germinated from the samples. In general, more seeds and taxa were observed in the drift at higher flows. By altering the period of peak flows from winter–spring to summer–autumn, flow regulation similarly affected the period of peak seed dispersal. The effect of regulation on seed dispersal varied between taxa depending on their timing of seed release and whether or not they maintain a persistent soil seed bank. 4. Hydrochory in rivers is a product of flow regime and the life history of plants. By altering natural flow regimes and thus hydrochorous dispersal patterns, flow regulation is likely to affect adversely the recruitment of native plant species with dispersal phenologies adapted to natural flow regimes (such as many riparian trees and shrubs) and encourage the spread of non‐native (exotic) species. 5. Changes to hydrochorous dispersal patterns are an important mechanism by which altered flow timing affects riverine plant communities. Natural seasonal flow peaks (in this case spring) are likely to be important for the recruitment of many native riparian woody taxa.     

Effects of hydropower-induced flow perturbations on mayfly (Ephemeroptera) richness and abundance in north Swedish river rapids

Mayfly species richness and abundance were investigated at 52 Swedish river rapids. These were either unregulated, or regulated with or without reduced discharge. Sites impacted by regulation had lower mayfly richness and abundances than unregulated reference sites. The relative importance of reduced discharge, daily fluctuations in flow, flow constancy, and the distance to nearest rapid (as a measure of isolation) was evaluated in multiple regression analyses. These indicated negative effects of diel fluctuations on both abundance and richness, whereas flow constancy was favourable for richness. Neither the distance to nearest rapid nor reduced flow were significantly related to mayfly richness and abundance. In total, 26 mayfly species were recorded. Only Baetis rhodani was found at all sites, but another five species were present at more than 40 sites. The strongest effects were found for species within the Heptageniidae. Nineteen of 20 mayfly species present in both the regulated (with unreduced flow) and unregulated reference rapids were on average more common in the unregulated ones. Mayfly assemblage structure was primarily influenced by regional factors and nutrient status, although daily fluctuations in flow together with rapids dimensions also had a significant influence. No rare species appears to be threatened by hydropower regulation though it is conceivable that depressed abundances in regulated rivers indirectly influence predators and periphyton.     

Droughts and anti-droughts: the low flow hydrology of Australian rivers

1. Droughts are not easily defined other than by culturally driven judgements about the extent and nature of impact. Natural ecosystems are adapted to the magnitude and frequency of dry periods and these are instrumental in controlling the long term functioning of these systems. 2. In unregulated rivers, low flows are derived from water in long‐term storage in the catchment, commonly as shallow groundwater. Four types of low flow sequences are evident for representative rivers from each of the seven flow regime zones in Australia and an arid zone stream: perennial streams with low annual flow variability that have seasonal low flows but do not cease to flow; perennial streams with high annual variability that cease to flow in extreme years; ephemeral streams that regularly cease to flow in the dry season; and arid zone streams with long and erratic periods of no flow. 3. Although Australian rivers record runs of consecutive years of low flows longer than would be expected theoretically, the departures from the expected are not statistically significant. Trends and quasi‐cycles in sequences of low‐flow years are observed over decadal time scales. 4. Examples of the effects of river regulation on low flows in southern Australia indicate that, while in detail the impacts of regulation vary, in general regulation mitigates the severity of low flows. 5. It is our contention that the indigenous biota of Australian rivers are adapted to the naturally occurring low flow conditions and that, while there is considerable scientific interest in the effects of climate change on stream ecology, such studies have little practical relevance for the management of indigenous biota in unregulated rivers. 6. The changes brought about by the regulation of rivers are much more rapid and dramatic than those which might occur as a result of climate change and it is possible to develop management procedures to mitigate them. In regulated rivers, the real problem may be ‘anti‐droughts’– the removal of significant natural low‐flow events from the flow pattern.     

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.     

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.     

Assessing effects of flow alteration on macroinvertebrate assemblages in Australian dryland rivers

1. Possible impacts of water‐resource development on assemblages of freshwater macroinvertebrates were investigated in the upper Darling River and some of its tributaries in north‐western New South Wales (Australia), an arid and semi‐arid region of low relief where alteration of river flows has intensified through expansion of irrigated agriculture. 2. Study sites were grouped into four hydrological regimes resulting from impoundment, flow regulation, water abstraction and natural variation, namely (i) intermittent flow with relatively little hydrological alteration from water‐resource development, (ii) intermittent flow with substantial alteration, (iii) near‐perennial flow with substantial alteration but unimpounded and (iv) near‐perennial flow with substantial alteration plus impoundment by weirs that stabilise water levels. 3. Macroinvertebrates were sampled with three methods (a quantitative cylinder sampler, handnet sampling and baited traps) in three periods with differing hydrology (recessional low flow in June 2003, high flow in March 2004 and increasing flow after drought in December 2004). 4. Taxonomic richness, assemblage composition and catch per unit effort of the crayfish Cherax destructor differed significantly among the site groups, but total macroinvertebrate density and the AUSRIVAS O/E (Australian River Assessment System observed‐over‐expected) index did not. The principal spatial differences were between the intermittent and near‐perennial rivers, and apparent effects of water‐resource development and impoundment were more subtle. Temporal differences in richness, abundance and composition were substantial and appeared to be related mainly to variations in discharge and temperature. 5. Current macroinvertebrate‐based methods for assessing the ‘condition’ or ‘health’ of Australian dryland rivers are inadequate. Such assessments might be improved with (i) reference data that take adequate account of antecedent hydrological conditions, (ii) consideration of long‐term taxonomic richness as well as richness on individual sampling occasions, (iii) evaluation of invertebrate population sizes, (iv) analysis of assemblage data by trait composition and (v) adoption of the genus as the default level of taxonomic resolution.     

Linking Water Quality and Quantity in Environmental Flow Assessment in Deteriorated Ecosystems: A Food Web View

Most rivers worldwide are highly regulated by anthropogenic activities through flow regulation and water pollution. Environmental flow regulation is used to reduce the effects of anthropogenic activities on aquatic ecosystems. Formulating flow alteration–ecological response relationships is a key factor in environmental flow assessment. Traditional environmental flow models are characterized by natural relationships between flow regimes and ecosystem factors. However, food webs are often altered from natural states, which disturb environmental flow assessment in such ecosystems. In ecosystems deteriorated by heavy anthropogenic activities, the effects of environmental flow regulation on species are difficult to assess with current modeling approaches. Environmental flow management compels the development of tools that link flow regimes and food webs in an ecosystem. Food web approaches are more suitable for the task because they are more adaptive for disordered multiple species in a food web deteriorated by anthropogenic activities. This paper presents a global method of environmental flow assessment in deteriorated aquatic ecosystems. Linkages between flow regimes and food web dynamics are modeled by incorporating multiple species into an ecosystem to explore ecosystem-based environmental flow management. The approach allows scientists and water resources managers to analyze environmental flows in deteriorated ecosystems in an ecosystem-based way.     

Using fish guilds to assess community responses to temperature and flow regimes in unregulated and regulated Canadian rivers

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The ecology of rivers with contrasting flow regimes: identifying indicators for setting environmental flows

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Mechanisms of Riparian Cottonwood Decline Along Regulated Rivers

Decline of riparian forests has been attributed to hydrologic modifications to river flows. However, little is known about the physiological and structural adjustments of riparian forests subject to modified flow regimes, and the potential for forest restoration using historic flow regimes is poorly understood. In this paired river study, we compared hydrology, water relations, and forest structure in cottonwood-dominated floodplains of the regulated Green River to those of the unregulated Yampa River. We measured floodplain groundwater levels, soil water availability, cottonwood xylem pressure (Ψ_xp), and leaf-level stomatal conductance (g_s) to assess current impacts of river regulation on the water status of adult cottonwoods. We also simulated a flood on the former floodplain of the regulated river to evaluate its impact on cottonwood water relations. Canopy and root structure were quantified with estimates of cottonwood leaf area and percent live canopy and root density and biomass, respectively. Regulation of the Green River has lowered the annual peak flow yet raised minimum flows in most years, resulting in a 60% smaller stage change, and lowered soil water availability by as much as 70% compared to predam conditions. Despite differences in water availability, daily and seasonal trends in Ψ_xp and g_s were similar for cottonwoods on the regulated and unregulated rivers. In addition, soil water added with the experimental flood had little effect on cottonwood water relations, contrary to our expectations of alleviated water stress. Green River cottonwoods had 10%–30% lower stand leaf area, 40% lower root density, and 25% lower root biomass compared with those for Yampa River cottonwoods. Our results suggest that water relations at the leaf and stem level are currently similar for Yampa and Green River trees due to structural adjustments of cottonwood forests along the Green River, triggered by river regulation.     

Resizing a River: A Downscaled,Seasonal Flow Regime Promotes Riparian Restoration

While riverine organisms are adapted to the natural flow regime, it is impractical to fully restore natural flows along most regulated rivers. We propose an alternative with the delivery of downscaled flow regimes that provide the seasonal patterns that are essential for aquatic and riparian ecosystems. The Bridge River in British Columbia provided a novel case study as a downscaled flow regime commenced in 2000 along a reach that had generally experienced no flow for the prior half‐century. The experimental flow delivered a mean discharge of about 3 m³/s, versus the pre‐dam mean of 100 m³/s, with a seasonal pattern that mimicked the natural snowmelt‐dominated pattern. To assess the environmental response, we investigated black cottonwoods, Populus trichocarpa, the dominant riparian trees, in the pre‐flow versus post‐flow intervals, using tree ring interpretation for growth analyses and age determination. Sparse mature trees established prior to the 1948 damming did not show significant growth changes in the pre‐ versus post‐flow intervals. In contrast, younger trees that established closer to the river in the decade prior to 2000 displayed significant growth increases by 2002, and juveniles established after 2000 demonstrated faster initial growth than juveniles established before 2000. Further, bands of cottonwood saplings resulted from seedling recruitment along the new river fringe, particularly in 2002, 2003, and 2004, years with gradual flow recession. These responses demonstrate that a downscaled, seasonal flow regime provided environmental benefit, thereby restoring some river function and resulting in a resized river flanked by narrow and reproducing cottonwood bands.     

The effects of increased flow and fine sediment on hyporheic invertebrates and nutrients in stream mesocosms

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Dams and Flow in the Cotter River, Australia: Effects on Instream Trophic Structure and Benthic Metabolism

This study assessed benthic macroinvertebrates and periphyton and its responses to managed river-flows, in riffles downstream of three dams on the Cotter River, Australian Capital Territory. Benthic macroinvertebrates and periphyton were also assessed in adjacent tributaries of the river, as well as in a nearby unregulated river and its tributaries. Food sources of four macroinvertebrate taxa (Leptophlebiidae, Elmidae, Glossosomatidae and Orthocladiinae) were determined by stable isotope analysis of the invertebrates and their potential food, in conjunction with examination of the gut contents of individual invertebrates. Components of benthic periphyton were the main food source for the selected taxa. Orthocladiinae consumed primarily amorphous detritus, while Elmidae, Glossosomatidae and Leptophlebiidae consumed diatoms. Enclosed benthic chambers were used to measure the response of benthic metabolism to monthly flow spikes released from one of the dams. The balance of benthic metabolism as measured by the Production/Respiration ratio (P/R) showed a shift towards production after the release of flow spikes. At sites downstream of the dams, there was more periphyton chlorophyll-a in the form of filamentous green algae than at sites in the unregulated river and the tributaries, and macroinvertebrate taxa using periphyton as a food resource were missing or reduced in abundance relative to sites without dams. However, the site downstream of the dam with environmental flow releases had more macroinvertebrate taxa and less periphyton cholorophyll-a content than sites downstream of dams without managed environmental flows, suggesting that a more suitable food supply resulting from environmental flow releases shifted macroinvertebrate communities towards those of unregulated streams.     

Spatio-temporal effects of river regulation on habitat quality for Atlantic salmon fry

Many upland rivers in the Northern Hemisphere contain important habitat for Atlantic salmon (Salmo salar L.). Owing to their sensitivity to environmental change, salmon are often used as bio-indicators. In Scotland, rivers containing potentially suitable habitat for salmon fry are often also regulated for hydropower. Regulated flow regimes can differ substantially spatially and temporally. Thus, where river management may be needed to maintain, restore, and protect their ecological functioning, this needs to be based on evidence of such spatio-temporal effects. This study investigated the effects of different types of river regulation on the hydraulic characteristics of downstream river reaches and the inferred consequences for salmon fry using hydraulic habitat quality models. The study focussed on the River Lyon (390 km²), a tributary of the Tay (4587 km²), Scotland, UK. Hydraulic habitat variability was assessed for three reach-scale sites with contrasting flow regimes characterised by (a) releases from hydropower generation, (b) compensation flow and (c) partly re-naturalised flow conditions. For each site, high resolution Digital Terrain Models (DTMs) were developed from bathymetric surveys and 2D hydraulic models were used to assess hydraulic characteristics. Discharge time series were used to simulate hydraulic conditions for regulated and simulated natural flows. Depth and velocity data were extracted from the hydraulic models and used to infer habitat quality using a habitat model developed for Atlantic salmon fry in similar-sized Scottish rivers. Results showed the effects of regulation can vary substantially within reaches and between seasons. Comparison to natural flow regimes suggested that flow alteration has a variable influence on habitat quality depending on the type of regulation and time of year. This work has improved understanding of the effects of regulation on biophysical processes and may also be useful for managing trade-offs between management, restoration, and societal benefits.     

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.     

Pathways for algal recolonization in seasonally‐flowing streams

1. In semi‐arid climates, seasonally‐flowing streams provide most of the water required for human use, but knowledge of how water extraction affects ecological processes is limited. Predicted alterations in stream flows associated with the impacts of climate change further emphasize the need to understand these processes. Benthic algae are an important base for stream food webs, but we have little knowledge of how algae survive dry periods or respond to altered flow regimes. 2. We sampled 19 streams within the Grampians National Park, south‐eastern Australia and included four components: a survey of different drought refuges (e.g. permanent pools, dry biofilm on stones and dry leaf packs) and associated algal taxa; a survey of algal regrowth on stones after flows recommenced to determine which refuges contributed to regrowth; reciprocal transplant experiments to determine the relative importance of algal drift and regrowth from dry biofilm in recolonization; direct measurement of algal drift to determine taxonomic composition in relation to benthic assemblage composition. 3. Algae showed little specificity for drought refuges but did depend on them; no species were found that were not present in at least one of the perennial pool, dry biofilm or leaf pack refuges. Perennial pools were most closely correlated with the composition of algal assemblages once flows resumed, but the loss or gain of perennial pools that might arise from stream regulation is unlikely to affect the composition of algal regrowth. However, regulated streams were associated with strong increases in algal density in dry biofilm, including increased densities of Cyanobacteria. 4. A model for algal recolonization in seasonally‐flowing streams identified three pathways for algal recolonization (drift‐dependent, dry biofilm‐dependent and contributions from both), depending on whether streams are diatom‐dominated or dominated by filamentous algae. The model predicted the effects of changes to stream flow regimes on benthic algal recolonization and provides a basis for hypotheses testable in streams elsewhere.