This paper reviews the management challenges facing Malawi lakes and analyzes the management responses that have been developed to deal with these challenges. Malawi lakes are under considerable stress due to high population growth and increasing levels of poverty which have led to overexploitation of fishery resources. High rates of soil erosion in the lake catchments are increasing siltation of shallow lakes, deltas and embayments, affecting water quality and fish breeding habitats, thereby degrading fish production potential. This review further shows that past and current management approaches have focused on maximizing sustainable yield and have failed to adequately incorporate socio-ecological factors and broader lake catchment processes into fisheries management plans. This, in turn, led to the top-down development of fisheries laws and technical regulations which were difficult to enforce, increased conflict between resource users and fisheries managers, and failed to control fisheries over-exploitation and the collapse of the chambo (tilapia) and cyprinid fisheries. The paper recommends that the fisheries policy should be reviewed to focus on resilience of fisheries, environment and livelihoods. Policy makers should adopt integrated management planning to address the diverse interest of stakeholders in lake basins, as well as the ecological, socioeconomic and external factors threatening sustainability of lake ecosystems and livelihoods of dependent communities.