The influence of water levels on population characteristics of yellow perch, Perca flavescens (Mitchill), and walleye, Sander vitreus (Mitchill), was evaluated across a range of glacial lakes in north-eastern South Dakota, USA. Results showed that natural variation in water levels had an important influence on frequently measured fish population characteristics. Yellow perch abundance was significantly (P < 0.10) greater during elevated water levels. Yellow perch size structure, as indexed by the proportional size distribution of quality- and preferred-length fish (PSD and PSD-P), was significantly greater during low-water years, as was walleye PSD. Mean relative weight of walleye increased significantly during high-water periods. The dynamic and unpredictable nature of water-level fluctuations in glacial lakes ultimately adds complexity to management of these systems.