Streamflow alteration can degrade aquatic ecosystem health. However, determining acceptable levels of alteration is challenging when evaluating ecological risks across multiple species, life stages, and a diversity of stream types within a region. Natural resource managers need tools that can be applied at the watershed or regional scale to evaluate potential ecological consequences of flow alteration and to identify protective ranges of alteration. Risk-based approaches provide an advantage over traditional approaches of establishing environmental flow targets by providing the flexibility to adjust management objectives based on risk tolerance, the needs of different species, and trade-offs with other water demands. In this study, we developed an ecological risk assessment framework for identifying protective ranges of flow alteration, leveraging existing studies and datasets to account for varying risk profiles of specific species and life-stages of interest. We evaluated changes in regional ecological risks associated with incremental deviations from unimpaired flow for different species life-stage needs and under different annual climate conditions and physical channel settings. The framework is designed to protect the habitat needs of salmonids, such as Chinook salmon and steelhead trout, alongside other ecological endpoints including amphibians, benthic macroinvertebrates, and algal communities. This multi-species approach enables assessment of how flow alteration may affect both species of primary management concern, and the broader ecological functions supported by the natural hydrograph. We applied this framework in a coastal watershed in northern California, USA, synthesizing ecological risk curves to reveal inflection points that suggest levels at which diversion rate limits could be established. These insights can help inform regional flow management policies that balance human water use with aquatic ecosystem protection.