Nature development in The Netherlands is often planned on contaminated soils or sediments. This contamination may present a risk for wildlife species desired at those nature development sites and must be assessed by specific risk assessment methods. In a previous study, we developed a method to predict ecological vulnerability in wildlife species by using autecological data and expert judgment; in the current study, this method is further extended to assess ecological vulnerability of food chains and terrestrial and aquatic habitats typical for The Netherlands. The method is applied to six chemicals: Cd, Cu, Zn, dichlorodiphenyltrichloroethane, chlorpyrifos, and ivermectin. The results indicate that species in different food chains differ in vulnerability, with earthworm-based food chains the most vulnerable. Within and between food chains, vulnerability varied with habitat, particularly at low trophic levels. The concept of habitat vulnerability was applied to a case study of four different habitat types in floodplains contaminated with cadmium and zinc along the river Dommel, The Netherlands. The alder floodplain forest habitat contained the most vulnerable species. The differences among habitats were significant for Cd. We further conclude that the method has good potential for application in mapping of habitat vulnerability.