Annual cycle and inter-annual variability of gross primary production and ecosystem respiration in a floodprone river during a 15-year period

1. Temporal variation in ecosystem metabolism over a 15‐year period (1986–2000) was evaluated in a seventh order channelised gravel bed river (mean annual discharge 48.7 m³ s^?1) of the Swiss Plateau. The river is subject to frequent disturbance by bed‐moving spates. Daily integrals of gross primary production (GPP) and ecosystem respiration (ER) were calculated based on single‐station diel oxygen curves. 2. Seasonal decomposition of the time series of monthly metabolism rates showed that approximately 50% of the variation of GPP and ER can be attributed to season. Annual GPP averaged 5.0 ± 0.6 g O₂ m^?2 day^?1 and showed no long‐term trend. 3. Ecosystem respiration, averaging 6.2 ± 1.4 g O₂ m^?2 day^?1, declined from 8.8 to 4.1 g O₂ m^?2 day^?1 during the 15‐year period. This significant trend paralleled a decline in nitrate and soluble reactive phosphorus concentrations, and the biochemical oxygen demand discharged by sewage treatment facilities upstream of the study reach. The ratio of GPP to ER (P/R) increased from 0.53 to about 1 as consequence of ER reduction. 4. Bed moving spates reduced GPP by 49% and ER by 19%. Postspate recovery of GPP was rapid between spring and autumn and slow during winter. Recovery of ER lacked any seasonal pattern. Annual patterns of daily GPP and to a minor extent of daily ER can be described as a sequence of recovery periods frequently truncated by spates. 5. The study showed that disturbance by frequent bed‐moving spates resulted in major stochastic variation in GPP and ER but annual patterns were still characterised by a distinct seasonal cycle. It also became evident that stream metabolism is a suitable method to assess effects of gradual changes in water quality.     

The influence of native replanting on stream ecosystem metabolism in a degraded landscape: can a little vegetation go a long way?

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The Metabolic Regimes at the Scale of an Entire Stream Network Unveiled Through Sensor Data and Machine Learning

Streams and rivers form dense networks that drain the terrestrial landscape and are relevant for biodiversity dynamics, ecosystem functioning, and transport and transformation of carbon. Yet, resolving in both space and time gross primary production (GPP), ecosystem respiration (ER) and net ecosystem production (NEP) at the scale of entire stream networks has been elusive so far. Here, combining Random Forest (RF) with time series of sensor data in 12 reach sites, we predicted annual regimes of GPP, ER, and NEP in 292 individual stream reaches and disclosed properties emerging from the network they form. We further predicted available light and thermal regimes for the entire network and expanded the library of stream metabolism predictors. We found that the annual network-scale metabolism was heterotrophic yet with a clear peak of autotrophy in spring. In agreement with the River Continuum Concept, small headwaters and larger downstream reaches contributed 16% and 60%, respectively, to the annual network-scale GPP. Our results suggest that ER rather than GPP drives the metabolic stability at the network scale, which is likely attributable to the buffering function of the streambed for ER, while GPP is more susceptible to flow-induced disturbance and fluctuations in light availability. Furthermore, we found large terrestrial subsidies fueling ER, pointing to an unexpectedly high network-scale level of heterotrophy, otherwise masked by simply considering reach-scale NEP estimations. Our machine learning approach sheds new light on the spatiotemporal dynamics of ecosystem metabolism at the network scale, which is a prerequisite to integrate aquatic and terrestrial carbon cycling at relevant scales.

     

Climate-Induced Changes in Spring Snowmelt Impact Ecosystem Metabolism and Carbon Fluxes in an Alpine Stream Network

Although stream ecosystems are recognized as an important component of the global carbon cycle, the impacts of climate-induced hydrological extremes on carbon fluxes in stream networks remain unclear. Using continuous measurements of ecosystem metabolism, we report on the effects of changes in snowmelt hydrology during the anomalously warm winter 2013/2014 on gross primary production (GPP), ecosystem respiration (ER), and net ecosystem production (NEP) in an Alpine stream network. We estimated ecosystem metabolism across 12 study reaches of the 254 km² subalpine Ybbs River Network (YRN), Austria, for 18 months. During spring snowmelt, GPP peaked in 10 of our 12 study reaches, which appeared to be driven by PAR and catchment area. In contrast, the winter precipitation shift from snow to rain following the low-snow winter in 2013/2014 increased spring ER in upper elevation catchments, causing spring NEP to shift from autotrophy to heterotrophy. Our findings suggest that the YRN transitioned from a transient sink to a source of carbon dioxide (CO₂) in spring as snowmelt hydrology differed following the high-snow versus low-snow winter. This shift toward increased heterotrophy during spring snowmelt following a warm winter has potential consequences for annual ecosystem metabolism, as spring GPP contributed on average 33% to annual GPP fluxes compared to spring ER, which averaged 21% of annual ER fluxes. We propose that Alpine headwaters will emit more within-stream respiratory CO₂ to the atmosphere while providing less autochthonous organic energy to downstream ecosystems as the climate gets warmer.     

Metabolic regimes of three mid-order streams in southern Ontario,Canada exposed to contrasting sources of nutrients

Light, temperature, and discharge control stream metabolism, but the response of gross primary production (GPP) and ecosystem respiration (ER) to seasonal variation in these physical drivers may differ in accordance with the types of human activities present in the catchment. Our study examined three mid-order streams in southern Ontario, Canada that differed in anthropogenic nutrient sources (i.e., sewage treatment plant effluent, sewage lagoon effluent, and agriculture), but had comparable light, temperature, and discharge regimes. For each stream, GPP and ER were estimated daily from June through November. Comparisons of paired daily metabolic rates revealed pairwise differences among all streams, with streams receiving sewage effluent having greater rates and variability of GPP and ER than the stream draining agricultural land. The two sewage influenced streams differed only in ER. Temporal patterns of GPP and ER were correlated for all streams throughout the study period and were most affected by seasonal variation in temperature, whereby effluent receiving streams responded more rapidly to increases in temperature. Our findings suggest that managers may need to balance effects of human activities with regional environmental constraints on stream metabolism to maintain and enhance the ecological condition and services of stream ecosystems.

     

Multi‐scaled drivers of rural prairie stream metabolism along human activity gradients

1. Stream metabolism is increasingly used for monitoring and assessment of the biological condition of aquatic ecosystems. However, distal environmental drivers, such as land use, are typically not well connected to the proximate controls, such as stream chemistry, that are usually invoked as driving metabolism. This is particularly true for North American prairie streams and for grassland streams worldwide. 2. Stream metabolism was measured at the outflow of 19 subcatchments of the Red River in southern Manitoba, Canada. Subcatchments represented gradients of nutrient‐producing human activities present in the region, that is, wastewater treatment (WWT), livestock production and crop cultivation. Stream metabolism was estimated at all sites using diel changes in dissolved oxygen (DO) concentration over 1 week in the middle of summer. Environmental parameters hypothesised to control stream metabolism were sampled across three spatial scales (stream reach, stream segment and catchment). Model selection using Akaike’s information criterion (AIC) was used to determine linkages between environmental parameters and measures of stream metabolism. 3. Estimated rates of metabolism were within the range of past studies of metabolism in prairie streams, although most streams had negative values of net ecosystem metabolism. However, production‐to‐respiration ratios were >0.5, at all but three sites suggesting that autochthonous production was an important source of organic matter. 4. The a priori model that best predicted gross primary production (GPP) was the intensity of nutrient‐producing human activities (i.e. WWT, livestock and crop cultivation) measured at the catchment scale. Ecosystem respiration (ER) was best predicted by the a priori model comprised of GPP, total nitrogen (TN) and total phosphorus (TP). However, model averaging revealed that prediction of ER could be improved by including riparian cover and removing TP from the model. The positive association between GPP and ER suggested that heterotrophic compartments of the ecosystem were modest contributors to variation in respiration rates. 5. Overall, this study suggests that variation of metabolism in prairie streams of southern Manitoba is controlled by human activities occurring at the catchment scale, a finding consistent with current hierarchically structured riverine paradigms. Moreover, increased understanding of the hierarchical structure of stream metabolism drivers will help to ensure that assessment results can be used more effectively to inform management strategies for prairie ecosystems.     

Inter‐regional comparison of land‐use effects on stream metabolism

1. Rates of whole‐system metabolism (production and respiration) are fundamental indicators of ecosystem structure and function. Although first‐order, proximal controls are well understood, assessments of the interactions between proximal controls and distal controls, such as land use and geographic region, are lacking. Thus, the influence of land use on stream metabolism across geographic regions is unknown. Further, there is limited understanding of how land use may alter variability in ecosystem metabolism across regions. 2. Stream metabolism was measured in nine streams in each of eight regions (n = 72) across the United States and Puerto Rico. In each region, three streams were selected from a range of three land uses: agriculturally influenced, urban‐influenced, and reference streams. Stream metabolism was estimated from diel changes in dissolved oxygen concentrations in each stream reach with correction for reaeration and groundwater input. 3. Gross primary production (GPP) was highest in regions with little riparian vegetation (sagebrush steppe in Wyoming, desert shrub in Arizona/New Mexico) and lowest in forested regions (North Carolina, Oregon). In contrast, ecosystem respiration (ER) varied both within and among regions. Reference streams had significantly lower rates of GPP than urban or agriculturally influenced streams. 4. GPP was positively correlated with photosynthetically active radiation and autotrophic biomass. Multiple regression models compared using Akaike’s information criterion (AIC) indicated GPP increased with water column ammonium and the fraction of the catchment in urban and reference land‐use categories. Multiple regression models also identified velocity, temperature, nitrate, ammonium, dissolved organic carbon, GPP, coarse benthic organic matter, fine benthic organic matter and the fraction of all land‐use categories in the catchment as regulators of ER. 5. Structural equation modelling indicated significant distal as well as proximal control pathways including a direct effect of land‐use on GPP as well as SRP, DIN, and PAR effects on GPP; GPP effects on autotrophic biomass, organic matter, and ER; and organic matter effects on ER. 6. Overall, consideration of the data separated by land‐use categories showed reduced inter‐regional variability in rates of metabolism, indicating that the influence of agricultural and urban land use can obscure regional differences in stream metabolism.     

Prediction and assessment of local stream habitat features using large-scale catchment characteristics

1. Knowledge of what a habitat should be like, in the absence of the effects of human activities, is fundamental to local stream habitat assessment. It has been suggested that stream habitats are influenced by large-scale catchment features. This study aimed to identify these relationships so that local-scale habitat features could be predicted from larger-scale characteristics.
2. Fifty-one reference sites from the Upper Murrumbidgee River catchment, south-eastern Australia, were classified on the basis of the local features of their stream habitat. Large-scale variables, namely catchment area, stream length, relief ratio, alkalinity, percentage of volcanic rocks, percentage of metasediments, dominant geology and dominant soil type, provided sufficient information for classifying 69% of reference sites into appropriate reference site groups.
3. A model created using these large-scale catchment variables was able to predict the local habitat features that were expected (E) to occur at a site in the absence of the effects of human activities. These were compared with observed (O) local habitat features to provide an observed-to-expected (O/E) ratio, an assessment score of the habitat at a site. The departure of this ratio from 1 enables identification of those sites that may be impacted. A list of habitat features that are expected at a site can provide targets for habitat restoration or enhancement.
4. For impacted sites, when habitat assessment from the habitat predictive model was compared with biological assessment from the Australian River Assessment System (AUSRIVAS) predictive model, it was possible to identify whether habitat degradation or water quality degradation was the cause of biological impairment. Such assessment may make it possible to identify rehabilitation goals relevant to the biota.     

The seasonal dynamics and persistence of stream macroinvertebrates in Nepal: do monsoon floods represent disturbance?

1. The monsoon causes major flood events in some Himalayan streams, but their seasonal predictability might reduce the resulting disturbance. We assessed seasonal change in the benthos of 16 streams in central Nepal over a gradient of declining rainfall and increasing altitude from 600 to 3800 m. All sites were surveyed on four occasions, two in winter (November) and two pre-monsoon (June), with additional sampling during the monsoon (August) at four low altitude sites. Invertebrate abundance, taxon richness and persistence were assessed at all sites, and density and meso-habitat distribution at the four low altitude sites only.
2. Strong seasonal variation among invertebrates was confined primarily to streams at low altitude (600–800 m) where monsoon rainfall was greatest and catchments were dominated by terraced agriculture. At these sites, a significant reduction in benthic density (on average by 77%) and taxon richness (by 20%) occurred between the winter and pre-monsoon periods, so that invertebrate numbers were already low before the monsoon. A further significant decline occurred in all meso-habitats during the monsoon, but the change in density was small in absolute terms.
3. Persistence in rank abundance was equally low at all sites, but turnover in composition was significantly lower at sites in semi-natural forest than in catchments managed for terracing or alpine pasture.
4. These data provide no evidence that monsoonal floods represent major disturbance, instead supporting the view that the ecological response might reflect an adjustment to predictable flow pattern. However, catchment land use in the Himalaya appears to be a significant source of ecosystem instability, and confounds the simple interpretation of monsoon effects.     

Inter-biome comparison of factors controlling stream metabolism

1. We studied whole-ecosystem metabolism in eight streams from several biomes in North America to identify controls on the rate of stream metabolism over a large geographic range. The streams studied had climates ranging from tropical to cool-temperate and from humid to arid and were all relatively uninfluenced by human disturbances.
2. Rates of gross primary production (GPP), ecosystem respiration (R) and net ecosystem production (NEP) were determined using the open-system, two-station diurnal oxygen change method.
3. Three general patterns in metabolism were evident among streams: (1) relatively high GPP with positive NEP (i.e. net oxygen production) in early afternoon, (2) moderate primary production with a distinct peak in GPP during daylight but negative NEP at all times and (3) little or no evidence of GPP during daylight and a relatively constant and negative NEP over the entire day.
4. Gross primary production was most strongly correlated with photosynthetically active radiation (PAR). A multiple regression model that included log PAR and stream water soluble reactive phosphorus (SRP) concentration explained 90% of the variation in log GPP.
5. Ecosystem respiration was significantly correlated with SRP concentration and size of the transient storage zone and, together, these factors explained 73% of the variation in R. The rate of R was poorly correlated with the rate of GPP.
6. Net ecosystem production was significantly correlated only with PAR, with 53% of the variation in log NEP explained by log PAR. Only Sycamore Creek, a desert stream in Arizona, had positive NEP (GPP: R  > 1), supporting the idea that streams are generally net sinks rather than net sources of organic matter.
7. Our results suggest that light, phosphorus concentration and channel hydraulics are important controls on the rate of ecosystem metabolism in streams over very extensive geographic areas.     

Ecosystem metabolism and nutrient uptake in an urban,piped headwater stream

Piped streams, or streams that run underground, are often associated with urbanization. Despite the fact that they are ubiquitous in many urban watersheds, there is little empirical evidence regarding the ecological structure and function of piped stream reaches. This study measured ecosystem metabolism, nutrient uptake, and related characteristics of Pettee Brook—an urban stream that flows through several piped sections in Durham, New Hampshire, USA. Pettee Brook had high chloride and nutrient concentrations, low benthic biomass, and low rates of gross primary productivity (GPP), ecosystem respiration (ER), and nutrient uptake along its entire length during summer. Spring was a period of elevated biological activity, as increased light availability in the un-piped sections of the stream led to substantially higher GPP, ER, NH₄ uptake, and PO₄ uptake in these open reaches. Piped reaches of Pettee Brook were similar to open reaches in terms of water quality, dissolved O₂ concentration, temperature, and discharge. Piped reaches did, however, have significantly less light, shallower sediments, and no debris dams. The absence of light inhibited autotrophic activity in piped reaches, resulting in the complete loss of GPP as well as a significant reduction in benthic AFDM and chlorophyll a biomass. Heterotrophic activity in piped reaches was not impaired to the same extent as autotrophic activity. Reduced ER was observed in piped reaches during the summer, but we failed to find significantly lower DOC or nutrient uptake rates in piped reaches than in open reaches. Carbon consumption in piped reaches, which do not have significant autochthonous or allochthonous carbon replenishment, must rely primarily on upstream inputs of organic matter. These results suggest that although ecological conditions in piped streams may be degraded beyond the extent of other urban stream reaches, piped reaches may still sustain some measurable ecosystem function.     

Effects of aquatic plant management on stream metabolism and oxygen balance in streams

1. In unshaded, nutrient-rich streams, prolific growth of stream macrophytes often results in flows that over-top the banks and in high primary production and respiration that may result in extreme diel variations in dissolved oxygen. Consequently, water protection authorities commonly remove macrophytes periodically.
2. We investigated the effect of plant removal on stream metabolism and oxygen balance in two Swiss streams with a high macrophyte biomass. We monitored the concentration of dissolved oxygen before and after macrophytes were removed by cutting and dredging, and calculated rates of gross primary production and ecosystem respiration by means of diel oxygen curves.
3. The removal of plants, which had reached a dry biomass of 320–420 g m−2 immediately before plant removal, had a different impact on stream metabolism in the two streams. In the first (plants removed in May), neither primary production nor ecosystem respiration were significantly affected. In the second (plants removed in late July), gross primary production and ecosystem respiration were reduced by about 70%. In this latter stream gross primary production increased in the first 2 weeks after plant removal but never recovered to pre-disturbance levels.
4. The removal of plants coincided with only a moderate increase in nocturnal oxygen concentration (+1 mg L−1). This, and the rapid partial recovery of stream metabolism in the second stream, suggests that an increase in the oxygen concentration after plant cutting is transient in unshaded, nutrient-rich streams.     

Temperature and the metabolic balance of streams

1. It is becoming increasingly clear that fresh waters play a major role in the global C cycle. Stream ecosystem respiration (ER) and gross primary productivity (GPP) exert a significant control on organic carbon fluxes in fluvial networks. However, little is known about how climate change will influence these fluxes. 2. Here, we used a ‘natural experiment’ to demonstrate the role of temperature and nutrient cycling in whole‐system metabolism (ER, GPP and net ecosystem production – NEP), in naturally heated geothermal (5–25 °C) Icelandic streams. 3. We calculated ER and GPP with a new, more accurate method, which enabled us to take into account the additional uncertainties owing to stream spatial heterogeneity in oxygen concentrations within a reach. ER ranged 1–25 g C m^?2 day^?1 and GPP 1–10 g C m^?2 day^?1. The median uncertainties (based on 1 SD) in ER and GPP were 50% and 20%, respectively. 4. Despite extremely low water nutrient concentrations, high metabolic rates in the warm streams were supported by fast cycling rates of nutrients, as revealed from inorganic nutrient (N, P) addition experiments. 5. ER exceeded GPP in all streams (with average GPP/ER = 0.6) and was more strongly related to temperature than GPP, resulting in elevated negative NEP with warming. We show that, as a first approximation based on summer investigations, global stream carbon emission to the atmosphere would nearly double from 0.12 Pg C year^?1 at 13 °C to 0.21 (0.15–0.33) Pg C year^?1 with a 5 °C warming. 6. Compared to previous studies from natural systems (including terrestrial ecosystems), the temperature dependence of stream metabolism was not confounded by latitude or altitude, seasonality, light and nutrient availability, water chemistry, space availability (water transient storage), and water availability. 7. Consequently, stream nutrient processing is likely to increase with warming, protecting downstream ecosystems (rivers, estuaries, coastal marine systems) during the summer low flows from nutrient enrichment, but at the cost of increased CO₂ flux back to the atmosphere.     

Watershed-scale Land Use Change Increases Ecosystem Metabolism in an Agricultural Stream

Ecosystems - Stream metabolism, in the form of gross primary production (GPP) and ecosystem respiration (ER), is an important metric of stream ecosystem function, given GPP and ER are integrative...     

Effects of dilution stress on the functioning of a saline Mediterranean stream

The effects of seasonality and dilution stress on the functioning of Rambla Salada, a hypersaline Mediterranean stream in SE Spain, were evaluated. The stream is subject to diffuse freshwater inputs from the drainage of intensively irrigated agriculture in the catchment and periodic losses of water through an irrigation channel. Metabolic rates and the biomass of primary producers and consumers were estimated over a 2-year period. During the first year several dilution events occurred, while during the second year the salinity recovery reached predisturbance levels. Functional indicators were compared in the disturbance and recovery salinity periods. Primary production and respiration rates in the Rambla Salada ranged between 0.07–21.05 and 0.19–17.39 g O₂ m⁻² day⁻¹, respectively. The mean values for these variables were 7.35 and 5.48 g O₂ m⁻² day⁻¹, respectively. Mean net daily metabolism rate was 1.87 ± 0.52 g O₂ m⁻² day⁻¹ and mean production/respiration ratio was 2.48 ± 1.1, reflecting autotrophic metabolism. The metabolic rates showed the typical seasonal pattern of Mediterranean open canopy streams. Therefore, gross primary production (GPP) and ecosystem respiration (ER) registered maximum values in summer, intermediate values in spring and autumn and minimum values in winter. The metabolic rates and biomass of consumers were greater in the disturbance period than in the recovery period. However, they did not show significant differences between periods due to their important dependence on seasonal cycle. Seasonality accounted for much of the temporal variability in GPP and ER (76% and 83% in the multiregression models, respectively). Light availability seems to be the most important factor for GPP and ER in the Rambla Salada. Autotrophic biomass responded more to variations in discharge and conductivity than to seasonal variations. In fact, it was severely affected by freshwater inputs after which the epipelic biomass decreased significantly and Cladophora glomerata proliferated rapidly. Epipelic algal biomass was the most sensitive parameter to dilution disturbance. Handling editor: Luigi Naselli-Flores     

Assessing the performance of volunteers in monitoring streams

1. Citizens are concerned about the quality of water resources and many participate in monitoring activities, though doubts remain about the quality of the data volunteers collect. We trained volunteers to collect benthic macroinvertebrates using professional protocols. Of the seven stream sites sampled by volunteer crews, six sites were also sampled by professional crews.
2. In the laboratory, volunteers used morphological features to identify as many different taxa as possible within the major insect orders; their identification was approximately to family. Volunteers calculated five metrics: total taxon richness, richness of three key groups (Ephemeroptera, Plecoptera and Trichoptera), and percentage dominance of the three most abundant taxa. All metrics were strongly correlated with (a) the percentage of urbanized area in the catchment and (b) the metrics derived from a more complete taxonomic identification by a professional scientist. Taxon richness metrics declined with urban development, while percent dominance increased.
3. An overall summary multimetric index was used to compare the field and laboratory procedures of volunteers and professionals. Using an ANOVA model, we detected no significant difference between field samples collected by volunteers and professionals. The variance of index values associated with differences between crews was zero. The ability of the index to detect significant differences among sites (statistical power) improved by only 13% for assessments based on professional laboratory identification instead of volunteer laboratory identification.
4. Citizen volunteers, when properly trained, can collect reliable data and make stream assessments that are comparable to those made by professionals. Data collected by volunteers can supplement information used by government agencies to manage and protect rivers and streams.     

Flow regulation by dams affects ecosystem metabolism in Mediterranean rivers

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Flow extremes and benthic organic matter shape the metabolism of a headwater Mediterranean stream

1. Single‐station diel oxygen curves were used to monitor the oxygen metabolism of an intermittent, forested third‐order stream (Fuirosos) in the Mediterranean area, over a period of 22 months. Ecosystem respiration (ER) and gross primary production (GPP) were estimated and related to organic matter inputs and photosynthetically active radiation (PAR) in order to understand the effect of the riparian forest on stream metabolism. 2. Annual ER was 1690 g O₂ m^?2 year^?1 and annual GPP was 275 g O₂ m^?2 year^?1. Fuirosos was therefore a heterotrophic stream, with P : R ratios averaging 0.16. 3. GPP rates were relatively low, ranging from 0.05 to 1.9 g O₂ m^?2 day^?1. The maximum values of GPP occurred during a few weeks in spring, and ended when the riparian canopy was fully closed. The phenology of the riparian vegetation was an important determinant of light availability, and consequently, of GPP. 4. On a daily scale, light and temperature were the most important factors governing the shape of photosynthesis–irradiance (P–I) curves. Several patterns could be generalised in the P–I relationships. Hysteresis‐type curves were characteristic of late autumn and winter. Light saturation responses (that occurred at irradiances higher than 90 μE m^?2 s^?1) were characteristic of early spring. Linear responses occurred during late spring, summer and early autumn when there was no evidence of light saturation. 5. Rates of ER were high when compared with analogous streams, ranging from 0.4 to 32 g O₂ m^?2 day^?1. ER was highest in autumn 2001, when organic matter accumulations on the streambed were extremely high. By contrast, the higher discharge in autumn 2002 prevented these accumulations and caused lower ER. The Mediterranean climate, and in its effect the hydrological regime, were mainly responsible for the temporal variation in benthic organic matter, and consequently of ER.     

Stream channel geomorphology influences mussel abundance in southern Appalachian streams, U.S.A.

1. Studies of North American streams have shown that hydraulic parameters and stream geomorphology can explain unionid mussel abundance at both the reach and catchment scale. However, few studies have examined applicability of hydrogeomorphic variables across broader spatial scales, such as across whole catchments, or have elucidated conditions under which spates can affect mussel populations in streams. 2. We quantified freshwater mussel abundance and species richness and their physical habitat at 24 sites in eight streams in southern Appalachian catchments in 2000 and 2001. In addition, we modelled site‐specific hydraulic parameters during summer baseflow and bankfull stages to estimate high‐ and low‐discharge conditions, respectively. 3. Mussel abundance was related to stream geomorphology, whereas richness was related to stream size. Baseflow habitat parameters explained only minor variation in abundance or richness, and both measures were highly correlated with mean current velocity or stream size. Bankfull shear stress composed a relatively low proportion of overall mussel habitat variability, but it accounted for significant variation in abundance and richness. 4. Mussel abundance was highly variable at sites subject to low‐shear stress during spates, whereas abundance always was low at sites subject to high‐shear stress. These data suggest that habitat conditions during floods, rather than those at summer baseflow, limit the abundance of mussels in Appalachian streams. These data also suggest that mussel abundance and assemblage structure may be sensitive to any changes in channel geomorphology and hydraulic conditions that might result from land use in the catchment.