There is a growing consensus that ecohydrological and hydraulic-habitat tools should be combined when predicting the ecological effects of water management scenarios in rivers. We describe the principles of these technical tools, their predictive power, and their role within more general approaches for defining environmental water regimes. Using recent case studies, we illustrate how these tools quantify the expected impacts of hydrological and habitat alteration on aquatic communities, at the scale of stream reaches or whole catchments. In particular, we describe the potential of catchment-scale ecohydrological assessments for regionalizing environmental water regimes. We also illustrate the potential of spatially explicit habitat modeling at the reach scale for understanding the ecological effects of hydropeaking or morphological restoration. Finally, we show applications of hydraulic-habitat models at the catchment-scale. We discuss how ecohydrological and hydraulic-habitat approaches could be further developed to increase their biological realism and could be better integrated within modular platforms.