Since the Ramsar meeting in 1971 many plans and agreements are developed to conserve and improve the quality of wetlands throughout the world. Within the European Union for example legislation has been developed in four Directives which require thatwater managers test activities on ecological effects. Moreover, in most areas measures have to be taken and included in river basin management plans in order to achieve ecological objectives in terms of occurrence of species and habitats set by EU Directives. To improve quality and conserve areas it is needed to assess the effects of current land use and autonomous developments and to identify the effectiveness of measures. Different studies have already addressed the need for models to quantify these effects.We developed a conceptual framework to analyse the cause-effect chain from management to new environmental conditions and to the potential occurrence and quality of species and habitats using response curves. To our knowledge, this is the first framework presented that has the ecological assessments embedded within the structure, which allows for ecological assessments within the development of management plans rather than at the end of the development. For this purpose a spatial analysis tool is used (HABITAT), which is developed for a broad spectrum of users, from ecologists to managers, and purposes, from ecological assessments to flood risk assessments. The framework is applicable on an (inter) national scale and can promote the dialog between politicians, managers and ecologists. In this paper we demonstrate that the conceptual HABITAT framework for ecological impact assessment is able to support the development and implementation of ecologically sound management plans and illustrate this with a case study for the lake Markermeer in The Netherlands.