We developed an objective-based method for assessing environmental flows in estuaries; this method consists of two steps: identifying ecological objectives with temporal–spatial variability and establishing a relationship between variations in environmental factors and the alteration of freshwater inflows. Critical salinity and water depth requirements for different species in special seasons in addition to temporal variation in natural river discharge were combined as objectives with spatial and temporal variability. In a case study of the Yellow River Estuary, we determined that 15% and 101% of the natural river discharge should be provided to ensure the minimum and maximum levels of environmental flows, respectively, for successful integration of various objectives. Periods in early April, the end of June, August, and early October were identified as critical for fulfilling reasonable water requirements. Although the recommended environmental flows may not be ideal for certain types of species, they offer a boundary of environmental flows for preserving habitats and biodiversity in estuaries.