Migration is a widespread phenomenon in many ecosystems. Most often, studies on migration have focused on how migration strategies are dependent on ecological parameters, but little attention has been paid to the top-down effect of migration on ecosystem processes. Cyprinid fish in many European lakes undergo partial migration, where a part of the population leaves the lake and enters streams for the winter. In this study, we model the effect of partial migration by fish on lower trophic levels in a lake ecosystem. Our results suggest that spring phyto- and zooplankton dynamics, including occurrences of clear-water phases, can be related to the timing and magnitude of partial migration of planktivorous fish. From our results we conclude that partial migration can influence the dynamics of lower trophic levels in the ecosystem. Furthermore, we hypothesize that partial migration may affect the stability of alternative stable states and transitions between them.