This paper delivers a conceptual framework for the ecological functioning and biodiversity patterns of lakes that is based on the floodpulse concept (FPC). The specific characteristics of rivers and lakes considering water-level fluctuations are compared, with respect to catchment linkages, temporal patterns, and hydraulic forces of flooding and drawdown. The influences of floodpulses on element cycles, biodiversity, and adaptations of lake biota are analyzed, and the importance of multi-annual flooding cycles is highlighted. The degree by which these water-level fluctuations influence lake ecosystems strongly depends on lake morphology, where shallow lakes or those with large shallow margins are the most sensitive. Although floodpulses play a major role for ecosystem services such as lake management and climate change mitigation schemes, this issue is only scarcely dealt with. Tenets of the extended FPC for lakes are formulated in order to overcome this problem.