The response of various water quality parameters on nutrient load reduction in shallow lakes is often non-linear, because of the many different ecological interactions involved. In order to get insight into this, a mathematical model is presented combining a description of the internal nutrient cycles with a food-web approach. Different applications of the model are discussed: combined calibration on a multi-lake data set, and a study on the effects of increasing vs. decreasing loading on the water quality in an “average shallow lake”. The model has also been used to evaluate different restoration scenarios in several lakes in The Netherlands.