In the USA, the Habitat Evaluation Procedure (HEP) has become a standard approach for impact assessment and evaluation of measures and management activities causing changes in the environmental conditions of the habitats for fauna species. Recently, the method was implemented in The Netherlands. HEP is used to predict the ecological impact of measures and management activities concerning the ecological rehabilitation of rivers, tidal wetlands, lakes and marshes. For more than 30 fauna species the habitat requirements and preferences have been modelled. Examples of species-habitat relationships are presented. First results of the application of the method in ecological rehabilitation projects of rivers, lakes and marshes are presented. The results show that the HEP approach is a useful tool in ecological water management.