Habitat models are a possibility to improve the prediction of effects on the environment caused by any interventions or measures in the environment. The aim of this study is the development of a Geographical Information System (GIS) based spatial decision support framework for assessing the habitat quality for different species in an automated way. The framework relies on an integration of GIS, MCDM (multi-criteria decision making) methods, and sensitivity analysis. Both, habitat suitability maps, which spatially visualize the likelihood of one species’ occurrence, and statistical reports about the created maps, can be created with the help of the developed framework. All the functionalities provided by the framework are implemented as part of a toolbox for ArcGIS. The application of the developed GIS-based spatial decision support framework is illustrated by a case study, which focuses on semiterrestrial and terrestrial habitats along the two Austrian rivers “Gail” and “Mur”. Within this case study habitat suitability maps and statistical reports are created for four relevant index species in order to identify habitats that need to be protected.