Abstract. An integrated multi-objective method for environmental flow assessments was developed that considered variability of potential habitats as a critical factor in determining how ecosystems respond to hydrological alterations. Responses of habitat area, and the magnitude of those responses as influenced by salinity and water depth, were established and assessed according to fluctuations in river discharge and tidal currents. The requirements of typical migratory species during pivotal life-stage seasons (e.g., reproduction and juvenile growth) and natural flow variations were integrated into the flow-needs assessment. Critical environmental flows for a typical species were defined based on two primary objectives: (1) high level of habitat area and (2) low variability of habitat area. After integrating the water requirements for various species with the maximum acceptable discharge boundary, appropriate temporal limits of environmental flows for ecosystems were recommended. The method was applied in the Yellow River estuary in eastern Shandong province, China. Our results show that, while recommended environmental flows established with variability of potential habitats in mind may not necessarily benefit short-term survival of a typical resident organism on a limited temporal or spatial scale, they may encourage long-term, stable biodiversity and ecosystem health. Thus, short-term ecosystem losses may be compensated by significant long-term gains.