Water management is important for delivering water for different users and uses.Reservoirs are built to overcome the stochastic nature of river flows and to increase the reliability of water supply. Reservoir operation affects the ecology of downstream river sections, and there has been a discussion of a more ecologically oriented flow regime, although ecosystems of reservoirs themselves are rarely taken into account.For reservoirs, it is important to identify multiple impacts and trade-offs of different management options. This information can be used in a multidisciplinary and multiparticipatory decision-making process to assess the management options. This study develops, applies, and discusses reservoir operation options for the São Francisco River basin (Brazil): (a) Reference; (b) Environmental discharge; (c) Reduced daily water-level variation; and (d) Reduced annual water-level variation. In the simulation study, the operation option with reduced daily water-level variation in reservoirs turned out to be the most flexible, guaranteeing hydropower generation and water supply in the dry season, while considering the ecology of the reservoirs and rivers. The simulations are exemplary for decision makers, requiring further assessment after agreeing on priority setting.