The importance of lake ecosystems for waterfowl remains a topic of debate. In order to assess how temporal variations in lake features, specifically shifts between alternative stable states, may interact with the waterfowl fauna, we performed a long-term (22 years) study of the shallow Lake Krankesjon, southern Sweden. Lower total numbers of waterfowl occurred during periods with low macrophyte cover and turbid water, than when submersed macrophytes flourished and the water was clear. Some specific functional groups of waterfowl, such as herbivores, invertebrate, and fish feeders, showed a positive relation to clear water and high macrophyte cover. Hence, our data suggest that some migratory waterfowl may select lakes based on water quality, thereby adjusting their large-scale migratory routes. On the other hand, omnivorous waterfowl exhibited their highest abundances during turbid conditions. Furthermore, waterfowl not primarily relying on food from the lake showed no response to fluctuations in turbidity or macrophyte cover, but followed regional trends in population dynamics. In our study lake, L. Krankesjon, we estimated that waterfowl remove less than 3% of the macrophyte biomass during a stable clear-water state with lush macrophyte beds. However, during transition periods between alternative stable states, when macrophyte biomass is lower and the plants already stressed, the consumption rate of waterfowl may have a stronger effect on lake ecosystem functioning.