The effects of changing climatic and socioeconomic conditions on the water quality of the Elbe River were investigated using the deterministic model QSim. Since the impact of global change on river water quality marks the endpoint of various processes in the catchment and in the atmosphere, this study was performed within a network of interacting models that determined input parameters for water quality simulations. The development of phytoplankton and nutrient concentrations under conditions of global change was modeled along a 700 km stretch of the river. The simulations revealed a strong, scale-dependent effect of climate change on phytoplankton biomass, leading to a longitudinal shift of the dominating processes (primary productivity vs. respiration) along the river continuum. Under reduced flow, combined with increasing temperature and global radiation, phytoplankton biomass increased and phytoplankton maxima shifted in upstream direction, followed by higher system respiration rates in the adjacent downstream sections. In contrast, higher flow shifted the phytoplankton maximum toward the downstream sections. Even a drastic reduction of phosphorus inputs from anthropogenic sources had only limited influence on algal biomass, due to the ability of algal cells to store phosphorus. A strong reduction in P-inputs especially in the headwaters would be necessary to counterbalance the possible climate-induced effects on algal biomass.