Impact from groundwater abstraction on freshwater resources and ecosystems is an issue of sincere concern in Denmark and many other countries worldwide. In addition, climate change projections add complexity to the existing conflict between water demands to satisfy human needs and water demands required to conserve streams as biologically diverse and healthy ecosystems. Solutions to this intensifying conflict require a holistic approach whereby stream biota is related to their physical environment at catchment scale, as also demanded by the EU Water Framework Directive. In the present study, climate impacts on stream ecological conditions were quantified by combining a heat and mass stream flow with a habitat suitability modelling approach. Habitat suitability indices were developed for stream velocity, water depth, water temperature and substrate. Generally, water depth was found to be the most critical factor for the stream ecological conditions at Sjælland, and field measurements show that water temperature is rising to damaging levels during low flow summer conditions. Using downstream longitudinal modelling of water flow and water temperature, it is found that shading by riparian forest land use can in some cases restore water temperatures to tolerable levels. The sensitivity to climate change impacts on flow and temperature is evaluated and discussed.