Shallow lakes have the potential to switch between two alternative stable states: a clear macrophyte-dominated and a turbid phytoplankton-dominated state. Observational and experimental studies show that in some lakes herbivory by birds may severely decrease macrophyte biomass, while in other lakes, the removed biomass by herbivory is compensated by regrowth. These contradictory outcomes might arise because of interplay between top-down control by bird herbivory and bottom-up effects by nutrient loading on macrophytes. Here, we use the ecosystem model PCLake to study top-down and bottom-up control of macrophytes by coots and nutrient loading. Our model predicted that (1) herbivory by birds lowers the critical nutrient loading at which the regime shift occurs; (2) bird impact on macrophyte biomass through herbivory increases with nutrient loading; and (3) improved food quality enhances the impact of birds on macrophytes, thus decreasing the resilience of the clear-water state even further. The fact that bird herbivory can have a large impact on macrophyte biomass and can facilitate a regime shift implies that the presence of waterfowl should be taken into account in the estimation of critical nutrient loadings to be used in water quality management.