Water levels in freshwater reservoirs worldwide are changing due to altered climate, management practices, and increasing human demand for water. In the desert southwestern USA, managers are considering significant changes to reservoir operation strategies and water management in response to consumptive use and ongoing drought. To inform reservoir management decision-making, we reviewed current peer-reviewed literature to identify the effects of decreasing or increasing water level on phytoplankton, cyanobacteria, Escherichia coli, and Naegleria spp. We identified 34 studies containing 42 individual waterbodies that investigated the effects of water level increases or decreases on phytoplankton or cyanobacteria. We found that water level decreases resulted in a higher likelihood of increased cyanobacteria, and that phytoplankton were more likely to decrease in response to water level increases. Most of the waterbodies included in the literature review were eutrophic or hypereutrophic, underscoring the need to explore the effects of water level fluctuations on oligotrophic systems. We only identified five studies on E. coli through our review, and no studies on Naegleria spp. We supplemented our review with regional white papers and case studies within the Colorado River Basin and the Rio Grande River Basin to highlight relevant research. Prior and ongoing research highlights the need to explore impacts of water level fluctuations on phytoplankton and cyanobacteria to guide future management decision-making.