Managing rivers is becoming more challenging with increasing demand for better environmental flow regimes, just as demand for water for hydropower and water supply are increasing and water supplies are changing due to climate change. Restoration of freshwater ecosystems, such as in the Yuba River in California’s Sierra Nevada, will require flows that mimic the natural flow regime, which native freshwater species are uniquely adapted to. In particular, freshwater ecosystems of the Sierra Nevada were historically adapted to the spring snowmelt flows. To study the potential effects of restoring a natural flow regime to the Yuba River watershed, we developed a multi-reservoir network flow optimization model of the watershed that represents environmental flows more ecologically useful than simple minimum instream flows, which are typically the only environmental requirement in streams. The model uses weekly time steps. The objective function is to maximize benefit, which equals hydropower revenue less penalties for deviations from environmental constraints and spills. Constraints include targets for minimum flows, maximum flows, maximum weekly up-ramp rates and maximum weekly down-ramp rates. We applied the model to the Yuba River watershed surface water inflow data from a rainfall-runoff model recently developed for the Sierra Nevada that considers regional climate warming of +0, 2, 4 and 6 °C. The Yuba watershed has high potential for fish restoration yet is currently managed primarily for hydropower. We assess the economic effects (primarily impacts on hydropower generation and revenues in the adjacent Bear River) and management implications of increasing and reshaping instream flow requirements in several ecologically important, yet regulated, stream reaches within the Yuba watershed. Further, we explore the potential of using regulating reservoirs to adapt to changing hydrologic conditions. Increasing minimum instream flow magnitudes in the South Fork Yuba River reduces total hydropower generation and revenues by limiting diversions for hydropower. However, imposing environmental flow requirements to more closely mimic the natural flow regime, including spring snowmelt flows, results in much greater hydropower reductions due to reduced operational flexibility. Regulating reservoirs can preserve some components of the natural flow regime, but are not able to compensate for anticipated climate change-induced reductions in total annual flows. The general model is useful for making quantitative and qualitative assessments of potential new environmental flow requirements. With some key improvements, such as considering sub-weekly ramping rates, and adaptation for use elsewhere, the model can provide insights to water resources decision-makers about impacts of imposing different environmental flow conditions on watershed-scale water management schemes.