Human water demand combined with increasing frequency and severity of droughts brings river ecosystem needs into competition with human needs. Water managers face heightened challenges during these times, with strains on their ability to supply water and pressure from stakeholders to recognize and manage for aesthetic, recreational, and ecological values of rivers. To understand the ecological impacts of low-flow or drought periods in perennial systems, I reviewed literature on algae, aquatic invertebrates, and fishes to determine whether there were predictable responses. I found that algae tended to increase, while macroinvertebrates and fishes tended to decline, but there was great variability in these trends. Factors such as low-flow duration only explained a portion of this variability. I applied the results to the Upper Flint River Basin to examine likely changes during past droughts, and to provide recommendations to water managers for future droughts.