Modelling the effects of dam removal on migratory walleye (Sander vitreus) early life‐history stages

Many dams in the USA have outlived their intended purpose and an increasing number are being considered for removal. Yet, quantitative studies of the potential physical, biological and ecological responses are needed to assess dam removal decisions. In this paper, the responses of migratory walleye (Sander vitreus) to increased spawning habitat availability as a result of dam removal was studied by comparing scenarios with and without a high‐head dam in the Sandusky River (Ohio), a major tributary to Lake Erie. A conceptual, ecological model was proposed to define the relationship between hydrodynamics and walleye spawning, egg hatching, larval drift and survival. A mathematical, ecological model of the early life‐history stages was then developed and coupled with time series of depth and velocity predictions over the spawning grounds from a 1‐D hydrodynamic model. Model simulations were run for 1984–1993 for both the with‐ and without‐dam scenarios to assess the potential benefit of dam removal. The simulation results demonstrated that velocity, depth and water temperature are major factors influencing adult walleye spawning success. Without the dam, 10 times the amount of spawning habitat would be available for walleye to spawn. This increase in spawning habitat area resulted in up to five times the total egg deposition and seven times the larval output to the nursing grounds, based on the assumption that 5% of the walleye population of Lake Erie migrated up the Sandusky River to spawn. We concluded that the spawning habitat in the current condition (with the dam) is limiting and additional spawning habitat upstream could significantly increase the number of larval walleye drifting to Lake Erie. The model sensitivity analysis showed that the number of walleye migrating up the river in spring is the dominant factor for larval recruitment to the lake. Copyright © 2006 John Wiley & Sons, Ltd.     

Redds of brown trout in the deep channels of a hydroelectric power station

Natural spawning redds of brown trout were surveyed for the first time in 1?6‐m deep urban channels of a hydroelectric power station (HEP) between two lakes in Finland, by scuba diving and wading. Before damming a century ago, thousands of lake migrating trout spawners ascended through the rapids to upstream spawning areas. Between 2015 and 2018, 11 trout redds were observed at depths of 250?340 cm; these may be the deepest reported in running waters. Nine redds were found at depths of 75?230 cm. The nearest redds were situated only 55 m upstream and 110 m downstream from the HEP inflow and outflow, respectively. Channel substrate and trout redds were dominated by particle size classes 32?64, 64?128, and 16?32 mm. The risk of diving in the area increased due to the high amount of litter on the riverbed. Observations of wild trout parr by local anglers provide evidence that natural spawning produces some fish in the HEP channels.     

Migratory salmonid redd habitat characteristics in the Salmon River,New York

Non-native migratory salmonids ascend tributaries to spawn in all the Great Lakes. In Lake Ontario, these species include Chinook salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch), steelhead (O. mykiss), and brown trout (Salmo trutta). Although successful natural reproduction has been documented for many of these species, little research has been conducted on their spawning habitat. We examined the spawning habitat of these four species in the Salmon River, New York. Differences in fish size among the species were significantly correlated with spawning site selection. In the Salmon River, the larger species spawned in deeper areas with larger size substrate and made the largest redds. Discriminant function analysis correctly classified redds by species 64–100% of the time. The size of substrate materials below Lighthouse Hill Dam is within the preferred ranges for spawning for these four species indicating that river armoring has not negatively impacted salmonid production. Intra-specific and inter-specific competition for spawning sites may influence redd site selection for smaller salmonids and could be an impediment for Atlantic salmon (S. salar) restoration.     

Modelling changes in trout habitat following stream restoration

Stream restoration was implemented on the Upper Arkansas River near Leadville, Colorado, to improve brown trout (Salmo trutta) populations. Metals pollution and channel disturbance associated with historic mining, land use, and water development degraded aquatic and riparian habitat. Changes in instream habitat quality following restoration were investigated with a before–after–control–impact study design. Baseline, as‐built, and effectiveness surveys were conducted in 2013, 2014, and 2016, respectively. Two‐dimensional hydrodynamic modelling with River2D was used to estimate weighted usable area (WUA) for adult, juvenile, fry, and spawning brown trout across a range of flows. WUA was calculated from habitat suitability curves for velocity, depth, and channel substrate. Foraging positions (FP) and habitat heterogeneity were also evaluated as indices of habitat quality. All results were analysed with analysis of variance. At impact sites, WUA increased by 12.2% from 2013 to 2014 but decreased by 10.2% from 2014 to 2016, whereas FP increased by 24.8% from 2013 to 2014 but decreased by 26.1% from 2014 to 2016. Spawning habitat increased 53.3% from 2014 to 2016 at impact sites. The 15.4% increase in depth variability from 2013 to 2016 indicates that habitat heterogeneity was enhanced at impact sites. No changes in WUA, FP, or habitat heterogeneity were observed at control sites. Although changes in WUA and FP suggest that initial habitat improvements were not sustained, increased spawning habitat and depth heterogeneity suggest otherwise. Our results highlight the value of monitoring strategies that utilize multiple lines of evidence to evaluate restoration effectiveness, inform adaptive management, and improve restoration practices.     

GRAVEL AUGMENTATION INCREASES SPAWNING UTILIZATION BY ANADROMOUS SALMONIDS: A CASE STUDY FROM CALIFORNIA,USA

Anadromous salmonid diversity and abundance worldwide have been adversely impacted by anthropogenic forces, and millions of dollars are spent each year on stream habitat restoration and enhancement. However, there is a paucity of data comparing site use by salmonids before and after enhancement implementation, and few studies examine the specific environmental conditions that determine whether salmonids utilize an enhanced site. This study examines the use of gravel augmentation to improve spawning site utilization by Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) on the Lower American River, California, USA. Spawning increased across all augmentation sites for both species, although there were species‐specific and year‐specific differences in the degree to which a site was utilized and in the spatial distribution of redds in relation to substrate size, habitat features and other redds. There were also differences in redd architecture across sites that were related to differences in gravel size. This study illustrates that gravel augmentation projects can enhance spawning habitat for salmonids where spawning beds have degraded but that species‐specific and site‐specific attributes and gravel size can influence the relative effectiveness of a project. Copyright © 2013 John Wiley & Sons, Ltd.     

Influence of rainfall and beaver dams on upstream movement of spawning Atlantic salmon in a restored brook in Nova scotia,Canada

In a restored, third‐order stream in northern Nova Scotia, Canada, we used redd counts over 12 years to examine the influence of beaver dams and the timing and intensity of autumn rains on spawning activity of Atlantic salmon. Most beaver dams in most years had no detectable effect on the distribution of spawning redds, but in 2004 the density of redds downstream from a three‐dam complex was significantly greater than that above, suggesting the dams were a barrier to many fish. A second complex of dams blocked salmon passage completely in 2003 and 2004 until they were notched to provide access upstream. The length of stream used by salmon for spawning was linearly correlated with total precipitation in the basin in October plus November (R² = 0.60), to a ceiling of 325 mm, above which the fish had access to the entire brook, if beaver dams were notched. Number of redds in the whole brook was strongly correlated (R² = 0.94) with the coefficient of variation (CV) of daily rainfall in October, but only for 7 of 11 years. This relationship disappeared when the impassable beaver dam complex failed in 2005, allowing salmon free access to 4 km of the upper brook. Variation in rainfall, and hence discharge, in this flashy brook evidently influences migration and spawning of Atlantic salmon in conjunction with channel blocking by beaver dams. Copyright © 2009 John Wiley & Sons, Ltd.     

Multi-run migratory behavior of adult male lake sturgeon in a short river

Lake sturgeon (Acipenser fulvescens) can migrate long distances to spawn, but many populations currently spawn in systems where the length of accessible riverine migratory habitat has been greatly reduced by dam construction. With the increased prevalence of shortened rivers, focusing on migratory dynamics in short rivers (<30 km) is beneficial to understanding the migratory needs of lake sturgeon populations. Here we document male lake sturgeon movements during the spawning period in the Winooski River, Vermont, USA; a river with only 17 km to the first natural upstream barrier. Male lake sturgeon were acoustically tagged (n = 25, 1215–1470 mm TL) and tracked using five to nine stationary receivers from 2017 to 2019. River discharge, temperature, the lagged effect of temperature (3-day), and time of day were significant factors describing upstream movements of tagged fish. Migrating male lake sturgeon (n = 10 in 2017, n = 18 in 2018, and n = 17 in 2019) displayed general movement patterns during the spawning period that included a single run upstream to the spawning site (60%), upstream and downstream movements throughout the river during the season (20%), or multiple runs made up the entire length of the spawning tributary to the spawning site (20%). No multi-run males were observed during 2018 when discharge was less flashy (i.e., fewer steep increases and declines in discharge) than in 2017 and 2019. These results suggest that the prevalence of multi-run spawning behavior of male lake sturgeon is related to flow conditions.     

基于鱼类栖息地需求的雅鲁藏布江中游环境流量计算

针对水利工程影响下,河道下游天然水文情势改变造成鱼类产卵场面积减小和质量降低等潜在生态问题,通过数值模拟与统计建立拉萨裸裂尻鱼产卵期栖息地适宜度模型,采用栖息地模拟法计算了雅鲁藏布江中游藏木水电站坝下米林—尼洋河汇口处38.9 km河段的环境流量。结果表明:拉萨裸裂尻鱼产卵期适宜水深为0.7～1.0 m,适宜流速为0.4～0.6 m/s;研究河段内拉萨裸裂尻鱼产卵期环境流量为432 m~3/s。     

DISTRIBUTION AND ABUNDANCE OF STREAM FISHES IN RELATION TO BARRIERS: IMPLICATIONS FOR MONITORING STREAM RECOVERY AFTER BARRIER REMOVAL

Dams are ubiquitous in coastal regions and have altered stream habitats and the distribution and abundance of stream fishes in those habitats by disrupting hydrology, temperature regime and habitat connectivity. Dam removal is a common restoration tool, but often the response of the fish assemblage is not monitored rigorously. Sedgeunkedunk Stream, a small tributary to the Penobscot River (Maine, USA), has been the focus of a restoration effort that includes the removal of two low‐head dams. In this study, we quantified fish assemblage metrics along a longitudinal gradient in Sedgeunkedunk Stream and also in a nearby reference stream. By establishing pre‐removal baseline conditions and associated variability and the conditions and variability immediately following removal, we can characterize future changes in the system associated with dam removal. Over 2 years prior to dam removal, species richness and abundance in Sedgeunkedunk Stream were highest downstream of the lowest dam, lowest immediately upstream of that dam and intermediate farther upstream; patterns were similar in the reference stream. Although seasonal and annual variation in metrics within each site was substantial, the overall upstream‐to‐downstream pattern along the stream gradient was remarkably consistent prior to dam removal. Immediately after dam removal, we saw significant decreases in richness and abundance downstream of the former dam site and a corresponding increase in fish abundance upstream of the former dam site. No such changes occurred in reference sites. Our results show that by quantifying baseline conditions in a small stream before restoration, the effects of stream restoration efforts on fish assemblages can be monitored successfully. These data set the stage for the long‐term assessment of Sedgeunkedunk Stream and provide a simple methodology for assessment in other restoration projects. Copyright © 2011 John Wiley & Sons, Ltd.     

Seasonal selection of habitat by Spotted Bass and Shorthead Redhorse in a regulated river in the Midwest,USA

Riverine fish populations depend on habitats supporting their resource and life history needs. Dynamic streamflow caused by river regulation or natural events influences the distribution of downstream habitat characteristics. Through studying habitat selection, we can identify the most utilized and valuable habitats for the success of native fishes. We determined seasonal habitat selection of two common, native fish species on the Osage River downstream of Bagnell Dam, a hydroelectric dam in central Missouri, from April 2016 to June 2017 using radio telemetry. Spotted Bass (Micropterus punctulatus) are nest‐guarders, sight feeders, and habitat generalists, whereas Shorthead Redhorse (Moxostoma macrolepidotum) are fluvial dependent, migratory, and benthic feeders. Bayesian discrete choice analyses determined that both species selected particular water depth, velocity, and presence of submerged cover in some or all seasons, even as available habitat changed. Spotted Bass selected water depths <4.0 m near submerged cover during all seasons, low velocity during spring and summer, and near‐bank habitat in all seasons except spring. Shorthead Redhorse used fast flowing habitat during spring, 0.4–1.1 m/s velocity during summer, and low velocity in fall and winter (0.1–0.5 m/s). Shorthead Redhorse used submerged cover in all seasons except summer and selected specific ranges of depth within spring (2.4–4.4 m), summer (3.3–6.7 m), and winter (1.1–2.3 m). Our findings suggest that maintaining habitats with cover and diverse water depths and velocities, particularly both low and high velocity habitats during spring, may promote resilience by providing beneficial habitats for native fishes.     

Effects of Dam Removal on Tule Fall Chinook salmon Spawning Habitat in the White Salmon River,Washington

Condit Dam is one of the largest hydroelectric dams ever removed in the USA. Breached in a single explosive event in October 2011, hundreds‐of‐thousands of cubic metres of sediment washed down the White Salmon River onto spawning grounds of a threatened species, Columbia River tule fall Chinook salmon Oncorhynchus tshawytscha. We investigated over a 3‐year period (2010–2012) how dam breaching affected channel morphology, river hydraulics, sediment composition and tule fall Chinook salmon (hereafter ‘tule salmon’) spawning habitat in the lower 1.7 km of the White Salmon River (project area). As expected, dam breaching dramatically affected channel morphology and spawning habitat due to a large load of sediment released from Northwestern Lake. Forty‐two per cent of the project area that was previously covered in water was converted into islands or new shoreline, while a large pool near the mouth filled with sediments and a delta formed at the mouth. A two‐dimensional hydrodynamic model revealed that pool area decreased 68.7% in the project area, while glides and riffles increased 659% and 530%, respectively. A spatially explicit habitat model found the mean probability of spawning habitat increased 46.2% after dam breaching due to an increase in glides and riffles. Shifting channels and bank instability continue to negatively affect some spawning habitat as sediments continue to wash downstream from former Northwestern Lake, but 300 m of new spawning habitat (river kilometre 0.6 to 0.9) that formed immediately post‐breach has persisted into 2015. Less than 10% of tule salmon have spawned upstream of the former dam site to date, but the run sizes appear healthy and stable. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.     

Assessing habitat for lake sturgeon (Acipenser fulvescens) reintroduction to the Maumee River,Ohio using habitat suitability index models

Lake sturgeon (Acipenser fulvescens) were a candidate for reintroduction in the Maumee River, Ohio, where they were historically abundant, but are now functionally extirpated. Our objective was to determine if current habitat quality and quantity could support reintroduction efforts. We developed a spatially explicit habitat suitability index model for two lake sturgeon life stages: spawning adult and age-0 fish. To estimate habitat quality, substrate, water depth, and water velocity were assessed and integrated into suitability index values to delineate good, moderate, and poor areas for each life stage. Each habitat characteristic was mapped and combined to provide an overall assessment of habitat suitability, quantity, and location. Model results indicated 208 ha (10.2% of all habitat) of good adult spawning habitat (e.g., coarse substrates, depths between 0.3 and 8 m, and velocity between 0.5 and 1 m/s) and 529 ha (28.2% of all habitat) of good age-0 habitat (e.g., fine substrates, depths between 0.2 and 6 m, and velocity between 0.1 and 0.7 m/s). Good age-0 habitat was located mostly downstream of good spawning habitat, which will provide nursery areas for age-0 fish after hatch. Our models suggested habitat is not limiting for lake sturgeon and efforts to reintroduce this species into the Maumee River, and for the first time in the Lake Erie basin, were supported. The results of this work supported reintroduction efforts that began in 2018.     

Chinook salmon spawning surveys in deep waters of a large,regulated river

In 1986 research divers surveyed and mapped deep-water spawning redds of fall chinook salmon (Oncorhynchus tshawytscha) in selected sites within an impounded segment of the main-stem Columbia River, Washington State, U.S.A. In velocities over 3m s^?1 and depths up to 11 m, two divers riding a manoeuvrable sled made cross-current transects communicating observations of substrate materials and deep-water spawning sites. Surface personnel tracked the position of the sled with a laser locating system that logged the information into data storage. Subsequently, the computerized data were translated into overlaying maps depicting location of redds, substrate materials, and depth contours. Deep-water spawning (>3m) occurred at most survey sites in velocities between 0.6 and 0.8m s^?1. The average depth of spawning was 6.5 m, and the maximum was 9.1 m-deeper than the depth redds can normally be detected by aerial observation (3–4 m). Deep-water spawning ranged from none to substantial in areas of near identical physical characteristics. A method for estimating abundance and density of deep-water redds, based upon the data collected with this mapping technique, is presented. This study combined with current limited information concerning deep-water spawning suggests that up to 80 per cent of the escapement of fall chinook salmon in this reach may spawn in deep water.     

Downstream benthic responses to small dam removal in a coldwater stream

Increased awareness of the negative effects of dams combined with an aging dam infrastructure has led to an increase in dam removals. However, ecological responses of downstream biota to such actions are poorly understood. We examined the influence of a pair of small dam removals on downstream periphyton and macroinvertebrates in Boulder Creek, WI (USA). The dams were 180 m apart and both were removed on 9 July 2003. We monitored algae and macroinvertebrates as well as habitat characteristics for approximately 2 months before and after the removals upstream and downstream from the two dams, and continued our observations over a similar period (mid‐May to mid‐July) the following summer. After the removals, an initial release of sediment significantly increased the proportion of fine sediments in the downstream reach and buried benthic substrate. This burial led to a 60% reduction in chlorophyll in the downstream reach the week following removal, while concentrations increased in the upstream reference reach. Similarly, macroinvertebrate densities 2 weeks post‐removal were lower relative to pre‐removal densities and were associated with declines of ephemeropterans, trichopterans and dipterans. Examination of Trichoptera genera demonstrated substantial changes in this assemblage associated with diminished densities of the formerly dominant genus Brachycentrus. Algal and invertebrate populations increased in the weeks after the dam removal, but did not reach densities similar to the upstream reference reach. In the following year, both periphyton and invertebrate densities were lower in the downstream reach, suggesting a long‐term effect of the removal. Thus, effects of the dam removal were alternatively positive or negative over time, and indicate that the time scale of consideration has a strong effect on the interpretation of the consequences of this management activity. Copyright © 2008 John Wiley & Sons, Ltd.     

Specification of Flows for Flushing Surficial Sand from Cobble Riffles

Maintenance of habitat for benthic organisms and fish spawning may require flushing of sand from gravel or cobble river beds. An approach is proposed for specifying both the magnitude and duration of flow necessary to scour sand to a desired depth over a specified length of riffle bed. Scour is assumed to begin at the upstream end of the reach to be flushed and to progress downstream. The flow magnitude necessary for scour to an equilibrium depth was found from previously published laboratory data to be related to the median sand grain size and its movability number (the ratio of shear velocity to settling velocity). The required flow duration is determined by the time for scour to progress over the specified distance. The progression rate was determined through new laboratory experiments to be related to the flow velocity and depth, the distance advanced, the sand movability number and the channel slope. Application of the approach is illustrated by example. Copyright © 2015 John Wiley & Sons, Ltd.     

Quantifying Fish Habitat Associated with Stream Simulation Design Culverts in Northern Wisconsin

This study investigated the effects of culvert replacement design on fish habitat and fish weight by comparing substrate diversity and weight at three stream simulation (SS)‐design and three bankfull and backwater (BB)‐design sites on the Chequamegon‐Nicolet National Forest, Wisconsin. Stream channel cross‐sections, Wolman substrate particle counts, and single‐pass backpack electro‐fishing survey data were used to quantify fish habitat and fish weight in 50‐m upstream and downstream sample reaches at each site. We applied generalized linear mixed models to test the hypothesis that substrate size and fish weight did not differ according to stream‐crossing design type (SS or BB) and location (upstream or downstream). Substrate particle sizes were significantly greater upstream of the stream crossing when compared to downstream of the stream crossing at both SS and BB sites for riffles and pools. Substrate particle sizes were also significantly greater upstream of BB sites when compared to upstream of SS sites. Results of this study indicated statistically greater individual fish weights upstream of SS‐design sites in comparison to upstream of BB‐design sites in first‐ to third‐order low gradient streams. These results suggested that the SS‐design approach appears to be more effective at transporting sediment downstream, and illustrated the value of using fish weight as an indicator of biological success for stream‐crossing designs. Published 2017. This article is a U.S. Government work and is in the public domain in the USA. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.     

Spawning habitat of Atlantic salmon and brown trout: general criteria and intragravel factors

Generalized habitat criteria for spawning sites of Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) using depth, water velocity and substrate size were created based on published information. In addition, information on critical intragravel conditions for egg development was summarized. Salmon spawned mostly in relatively deep, swift‐velocity habitats (20–50 cm, 35–65 cm s^?1), whereas trout selected slightly shallower and slower flowing spawning sites (15–45 cm, 20–55 cm s^?1). Salmon and trout preferred pebbles (16–64 mm) for spawning. The minimum oxygen concentration for successful incubation of eggs varies with the developmental stage of eggs, and supply of it may be reduced by deposited fine sediment. Habitat criteria for spawning sites are narrower than those for small juveniles; therefore the use of separate criteria is recommended. In addition to the traditional habitat criteria variables (depth, water velocity, substrate), the critical intragravel factors affecting egg survival should be incorporated in biologically meaningful criteria for spawning habitat modelling. Copyright © 2008 John Wiley & Sons, Ltd.     

Migratory fishes of Brazil: Life history and fish passage needs

Many of the most important commercial and recreational species of the megadiverse Brazilian freshwater fishes migrate in rivers among essential habitats during all life stages. These movements, however, have been severely blocked by hundreds of hydroelectric dams and reservoirs and they will be even more obstructed due to hundreds of new developments. Fishways have been used in many countries to allow fish to pass around dams. Fishway construction is booming in Brazil, but poor understanding of migrations by Brazilian fishes has led legislators, scientists, and the public to several misconceptions about the rules of fishways in fisheries conservation. First, is a belief that fishways are only needed to facilitate upstream spawning migrations. Also, it has been suggested that upstream passage for Neotropical migrant fishes is not useful if there is no large free‐flowing stretch upstream of a dam that contains spawning habitat and has a large natural floodplain (nursery habitat). In this paper, we discuss that, in addition to providing passage for pre‐spawning migrants, upstream fishways also provide passage for other fish migrations (e.g. foraging), and that all up‐ and downstream migrations during life history need to be addressed at dams to conserve fish resources. We also argue that an upstream fishway is important even if the upstream reach does not have spawning or nursery habitats. In addition, we discuss the need for protection of downstream migrant fish, and the importance of fish behaviourists and engineers working together on fishway design and operation to solve fish passage issues. Copyright © 2008 John Wiley & Sons, Ltd.     

Restoration of Hydrochory Following Dam Removal on the Elwha River,Washington

Hydrochory, seed dispersal by water, affects riparian vegetation by contributing to downstream community composition and diversity. However, dams can block hydrochory, reducing downstream species diversity and fragmenting riparian corridors. Dam removal is becoming more prevalent for economic and ecological reasons and is expected to restore hydrochory; however, this has never been documented in rivers. The largest dam removal project to date was the 2011 to 2014 removal of the Glines Canyon and Elwha dams on the Elwha River in Washington. Prior to dam removal, hydrochory was lower below Glines Canyon Dam compared with an upstream reach; our objective was to test the hypothesis that dam removal would restore downstream hydrochory to levels observed in the upstream reach. To test this, we collected seeds in nets above and below the dam during three sample periods (early July, late July and early August), growing out seeds in a greenhouse and comparing seed abundance and species richness above and below dams, before and after dam removal. We found that after dam removal, the average number of hydrochorous seeds and species increased below Glines Canyon Dam to levels similar to or higher than that of the upstream reach; hydrochory levels in the upstream reach did not change. This study is the first to document the restoration of hydrochory in rivers following removal of a large dam. Restoration of hydrochory may ultimately increase downstream vegetation diversity and play a role in the recolonization of reservoir sediments deposited in the riparian zone in the years following dam removal. Copyright © 2016 John Wiley & Sons, Ltd.     

Development of Habitat Suitability Criteria and In‐Stream Habitat Assessment for the Benthic Cyanobacteria Phormidium

Global demand for freshwater has led to unprecedented levels of water abstraction from riverine systems. This has resulted in large alterations in natural river flows. The deleterious impacts of reduced flows on fish and macroinvertebrate abundances have been thoroughly investigated; in contrast, there is a limited understanding of the potential for changes in the abundance of nuisance benthic algal/cyanobacterial blooms. In New Zealand, Phormidium sp. blooms are common in numerous rivers during summer low flows. In this study, an in‐stream habitat assessment is used to examine the relationship between Phormidium habitat availability and reducing flows. Over 650 observations of Phormidium mats, from seven sites (Hutt River, lower North Island, New Zealand), were used to construct habitat suitability curves for depth, velocity and substrate. Preference curves were fitted using both the ‘forage ratio’ and ‘quantile regression’ methods. Phormidium growth, observed at all seven sites, increased significantly from upstream (uppermost site, 5.2% mat cover) to downstream (63.5%). The habitat suitability curves revealed Phormidium had a large tolerance to velocity, depth and substrate type. Consequently, decreases in flow had only negligible effects on available Phormidium habitat. During periods of stable flow, Phormidium abundance positively correlated with increased nitrogen concentrations, potentially explaining the large variation in Phormidium cover from upstream to downstream. Quantile regression generated habitat suitability criteria were a more accurate predictor of available Phormidium habitat than the forage ratio criteria. Copyright © 2013 John Wiley & Sons, Ltd.