A developing understanding of instream flow needs now supports maintenance of ecological flow regimes rather than a regulatory minimum flow. This shift is reflected in management of hydrologic alterations created by existing reservoirs and flow control structures. With an emphasis on regime-based approaches a new connectivity is demanded between reservoir operations and the resulting downstream flow conditions. Complicating this situation is reservoir management that may be legally limited to flood control and water supply requirements. This paper proposes an approach to reservoir operation that is based on an ecological flow regime. Reservoir operation is guided by six hydrologic indicators selected both to meet the specific flow needs of the local fish community and to satisfy authorized reservoir operational rules. The approach is based on use of an autecology matrix to meet flow needs of the ecology and life history requirements of the fish community. Optimization using non-dominated sorting genetic algorithms provides a basis for selecting flow regimes that are expected to provide benefit to fish communities downstream while also meeting authorized reservoir storage needs.