Most small scale inland fisheries worldwide are open access, and fishing provides the only source of employment and livelihood for the riparian communities. Management of these fisheries requires information on trade-offs between fish production, profits from fishing, employment, and conservation objectives. We use the non-linear optimization procedure in Ecopath with Ecosim (EwE) modelling package to determine long-term, gear-specific fishing effort that can maximize economic, social, and conservation objectives for Lake Victoria (East Africa). Then, the resulting “optimal fishing effort” levels are applied in both EwE and Atlantis models to simulate long-term changes in the ecosystem. Results show profit maximization to be more compatible with conservation objectives than is the maximization of catch (or employment). However, maximizing economic value, while maintaining ecosystem structure, would require a reduction in fishing effort of almost every fishing gear. This trade-off can be severe (high social cost) for fishing communities with limited alternative livelihoods. This study provides an understanding of relative risks and benefits of various management objectives, which will enable stakeholders and the public to conduct informed discussions on future management policies.