Predicting the environmental impact of a proposed development is notoriously difficult, especially when future conditions fall outside the current range of conditions. Individual-based approaches have been developed and applied to predict the impact of environmental changes on wintering and staging coastal bird populations. How many birds make use of staging sites is mostly determined by food availability and accessibility, which in the case of many waterbirds in turn is affected by water level. Many water systems are regulated and water levels are maintained at target levels, set by management authorities. We used an individual-based modelling framework (MORPH) to analyse how different target water levels affect the number of migratory Bewick’s swans Cygnus columbianus bewickii staging at a shallow freshwater lake (Lauwersmeer, the Netherlands) in autumn. As an emerging property of the model, we found strong non-linear responses of swan usage to changes in water level, with a sudden drop in peak numbers as well as bird-days with a 0.20 m rise above the current target water level. Such strong non-linear responses are probably common and should be taken into account in environmental impact assessments.