Hydrologic alteration is a pervasive issue globally. In many agricultural and urban areas, altered hydrology is the greatest risk factor associated with poor biological condition. Reducing the effects of hydrologic alteration require knowledge of expected change over large regions and timescales sufficient to inform management and regulatory decisions. This project developed tools to help managers evaluate the potential severity of effects of proposed actions that have the potential to alter flows and to inform decisions regarding stream protection, restoration, and management in light of anticipated flow alteration. The project estimated potential change to 10 functional flow metrics using Random Forest and related hydrologic alteration to the probability of adverse effects on benthic macroinvertebrates, benthic algae, and the sensitive arroyo toad. Finally, we developed a risk-decision framework to evaluate proposed projects or alternative future scenarios in terms of their likelihood to alter hydrology to a level that may impair aquatic life uses. Based on a combination of model performance and strength of relationships, we identified three priority flow metrics that were most associated with ecological effects: magnitude of largest annual storm and wet season baseflow and dry season baseflow magnitude. Expected hydrologic alteration for the two benthic communities evaluated resulted in between 25% and 79% of stream reaches being considered unhealthy based on hydrologic alteration. We used the model output to estimate limits of how much augmentation (+) or depletion (-) of flow can be tolerated to achieve at least the probability of adverse ecological effects. The limits can help flow managers understand the degree to which the current functional flows are altered and can inform decision making regarding project proposals that may alter functional flows. The resultant risk decision framework provides a process that managers can use to guide project evaluations and can easily be adapted for other areas.