Lake Malawi/Niassa/Nyasa (LMNN) is one of the most important and third-largest African Great Lakes. It has the largest number of freshwater fish species in the world, most of which are endemic. Current estimates put the number of fish species in the range of 800–1000. The riparian countries of Malawi, Mozambique and Tanzania enjoy enormous benefits that accrue from the ecosystem services that the lake provides. However, LMNN is experiencing severe adverse impacts resulting from anthropogenic and climatic stressors, leading to increased sediment and nutrient loading. This observation motivated this study to identify existing research gaps to enhance the lake’s sustainable management. Specifically, the assessment focused on three key issues identified and prioritised by the LMNN Basin Fisheries and Aquaculture Network (LMNNBFAN), namely: fishery health, invasive species, and climate change. Data collection involved stakeholder consultations, field surveys, and desk reviews. Recommendations from study findings, that would create a conducive environment for the sustainable management of the lake, have been grouped into four main categories: research needs, infrastructure development, human capacity building and funding.