Algal assemblage drives patterns in ecosystem structure but not metabolism in a productive river

Abstract Algal dynamics are fundamental drivers of lotic ecosystem processes. Although rivers tend to be heterotrophic and have low standing stocks of autotrophic biomass, filamentous algae can cause nuisance algal blooms that alter the structure of the autotrophic assemblage. Still, the influence of these blooms on ecosystem processes can be variable. Here, we examined the structural and functional contribution of filamentous and epilithic algae by linking algal biomass measurements to daily primary production fluxes throughout two growing seasons in six sites along the Upper Clark Fork River, an open canopy, snow melt river in western Montana, USA. We partitioned daily productivity estimates across different algal groups using the spatial and temporal variability in algal assemblages across our six sites. By using reach‐scale metabolism estimates, we assessed the in situ functional rates of individual algal groups. Throughout two growing seasons, we measured high fluxes of ecosystem productivity and spatially variable filamentous algal blooms. We found that the filamentous algal blooms determined the ecosystem structure in terms of total biomass and algal turnover times, but not the ecosystem functions of gross primary productivity, ecosystem respiration, or net production. Whole‐reach estimates of epilithic and filamentous algae growth rates were 0.30 and 0.026 day respectively, which are similar to rates measured in mesocosms. The epilithic algae grew and turned over rapidly, dominating total biomass production and driving ecosystem function while filamentous algae grew slowly and built up large amounts of biomass during a growing season, shaping the structure, but not function, of the ecosystem.