To access how multiple stressors affect the water quantity and quality and stream ecology at catchment scale under various management and climate change scenarios, we implemented macrophyte growth modules for the Soil and Water Assessment Tool version 2012 (SWAT). The macrophyte growth module originates from the INCA-P model (Wade et al. 2002) with an addition of nitrogen stress. In addition, a benthic sediment layer and interaction of nutrients between sediment layer and water column were implemented. The new modules were validated against macrophyte biomass measurements in several Danish streams. Sensitivity and uncertainty analysis of the new modules and different scenarios will reveal the impact of different stressors (temperature, nutrient levels, flow rate, etc.) on macrophyte growth.