Over the last decades, treatment of domestic wastewater promoted by environmental regulations have reduced human health risks and improved water quality. However, ecological risks caused by effluents of wastewater treatment plants (WWTPs) discharged into rivers still persist. Moreover, the evolution of these ecological risks in the future is intimately related to effects of changing climate, especially regarding streamflow in receiving rivers. Here, we present a systematic and transferable framework for assessing the ecological risks posed by individual WWTP-effluents at the catchment-scale. The framework combines the size-class k of WWTPs, which is a proxy for load, with the location of their outflows in river networks, represented by its stream-order ω. We identify ecological risks by using three proxy indicators: the urban discharge fraction and the local-scale concentrations of each total phosphorous and ammonium-nitrogen discharged from WWTPs. About 3,200 WWTPs over three large catchments (Rhine, Elbe, and Weser) in Central Europe were analyzed by incorporating simulated streamflow for the most extreme projected climate change scenario. We found that WWTPs causing ecological risks in future prevail in lower stream-orders, across almost all size-classes. Distinct patterns of ecological risks are identified in the k-ω framework for different indicators and catchments. We show that, as climate changes, intensified risks are especially expected in lower stream-orders receiving effluents of intermediate size WWTPs. We discuss implications of our findings for prioritizing WWTPs advancement and urging updates on environmental regulations. Further applications of the k-ω framework are discussed to help achieving global long-term commitments on freshwater security.