Macrophytes may enhance grazing on phytoplankton by providing a refuge for zooplankton against fish predation. Loss of macrophytes can trigger sudden degradation of water clarity (regime shift) in lakes. However, the presence of piscivores may drive planktivorous fish to take refuge amongst littoral macrophytes. To address the possibility of regime shifts, I here constructed an empirically based model that combined population dynamics of organisms with game theory for optimal habitat selection, taking into consideration the trophic structure, lake size and eutrophication. The model showed that macrophytes generally acted as a refuge for zooplankton, rather than for fish. The model predicted that regime shifts were more likely in small, shallow lakes and that the presence of macrophytes raised the possibility of regime shifts. The present study demonstrated that the fast dynamics of animal behaviour could lead to regime shifts, in connection with slower variables such as nutrient loading.