We constructed stream maps for a low-gradient trout stream in southwestern Virginia during autumn (base flow) and spring (elevated flows) to compare spatial and temporal variation in stream habitats. Pool–riffle sequencing and total area occupied by pools and riffles changed substantially depending on the level of discharge: reduced discharge resulted in an increase in total pool surface area with more numerous but smaller pools than during spring. In contrast, total surface area of riffles decreased with decreasing discharge as did total wetted surface area. These findings suggest caution should be exercised when comparing seasonal or annual surveys, applying habitat guidelines for assessment or management, evaluating fish standing crop potential from predictive habitat models, or predicting availability of habitat or biological information at times other than when stream surveys are conducted. We demonstrate the potential dangers by intentionally applying biological sample results taken at one discharge level to the same stream reach at a different discharge level. Our results clearly illustrate the importance of acquiring physical and biological information during similar discharges.