The variation in river discharge alters habitat heterogeneity with implications for the distribution of fish species with different habitat requirements. Assessments of habitat availability following changes in river discharge are difficult to apply at broad spatial scales and with relevance to multiple species. We used a MesoHABSIM modeling approach to quantify river-wide changes in habitat availability for five fish habitat guilds under three river discharge levels along the Niobrara River, NE, USA. We used a time-series of river discharge (1958−2010) to create uniform continuous under-threshold habitat duration curves that identified habitat conditions that may result in periods of stress for fish communities along the Niobrara River. Habitat availability for each fish habitat guild was dependent on river discharge and location along the river. Habitat availability for fish habitat guilds ranged from 5% to 49% of the total channel area suggesting habitat availability may, at times, be limited. We provide river discharge guidelines for bioperiods that limit the frequency and duration of stressful habitat conditions. Understanding interactions between river discharge and habitat availability through time and at river-wide scales may aid in managing for ecological integrity by including protection of river discharge variability to support multiple fish habitat guilds
