Study objectives After the implementation of EU's Water Framework Directive (WFD) in Denmark ecological impacts from groundwater exploitation on surface waters has to receive additional consideration. Small streams in particular are susceptible to changes in run-off but have only recieved little attention in past studies of run-off impact on the quality of stream physical habitats. This study combined catchment and instream models with instream habitat observations to assess the ecological impacts from groundwater exploitation on a small stream. The main objectives of this study was; • to assess which factors are controlling the run-off conditions in stream Ledreborg and to what degree • to assess the run-off reference condition of stream Ledreborg where intensive groundwater abstraction has taken place in 67 years using a simple rainfall-run-off-model • to assess how stream run-off affect the physical habitat quality of stream Ledreborg using af habitat hydraulic model • to assess the present and potential physical habitat quality of stream Ledreborg • to evaluate the suitability and applicability of habitat hydraulic models to Danish stream management Results • Precipitation and evaporation were the main factors controlling the overall run off variation and groundwater abstraction was controlling the lower limits for the low flows. The summer low flow is believed to be one of the main factors affecting biological quality of stream Ledreborg. From 1998-2002 the summer minimum and mean flow were 6.4-11.2 l/s and 21.7-78.3 l/s. Simulating a 'no-abstraction'-scenario the summer minimum and mean flow increased to 30-96 l/s and 60.1-151.5 l/s - assumed to be the summer run-off reference condition. On a yearly basis the scenario simulated a 25.4-82 l/s increase in mean flow. • Habitat observations showed that juvenile trout in stream Ledreborg prefered lower water depths and water velocities than juvenile trout in larger Danish streams, e.g. River Gudenå. Repeated electrofishing in the stream revealed big differences in temporal and spatial distribution of the trouts on the four reaches used for habitat hydraulic modelling. Results • Habitat hydraulic modelling revealed a much lower optimum flow when using site specific HSC's rather than general HSC's. •Temperature and O2-levels could to some level explain differences between potential physical habitat quality (WUA) at the reaches and abundance of trout on the reaches. • Comparison of reference condition minimum run-off and WUA curves suggested that summer low flow were not a limiting factor on the physical habitat quality for juvenile trout under reference conditions. • Habitat hydraulic modelling suggested that stream Ledreborg had the best potential physical habitat quality for trout fry and juvenile trout and the lowest potential physical habitat quality for adult trout. This finding supports previous evaluations of the stream as a trout habitat, concluding that stream Ledreborg has very few suitable habitats for adult trout. Conclusions • The NAM model could be applied to the Ledreborg catchment and estimate a reference condition with no groundwater abstraction. But more detailed groundwater models are needed for better analysis of groundwater impact on streams in areas with high groundwater abstraction levels. • Stream size (and possibly type) has an impact on HSC's from trouts of the same size, suggesting development of site specific HSC's for effective management and utilization of water ressources. • If habitat hydraulic models are to be used in Danish stream management, it would be useful to include water temperature in the modelling. • Although more time consuming than present Danish methods for assessment of physical habitat quality in streams, the habitat hydraulic models can be used to evaluate physical habitat conditions at reach level and work as a basis for a more objective assessment method.