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Fisheries resources face a confluence of socio‐ecological challenges, the resolution of which requires interdisciplinary scientific information for sustainable utilization and management. The present study assessed gaps and challenges in Lake Victoria fisheries resources management for better research focus, policy formulation and improved governance of the fishery towards sustainability. Using key informant interviews and a plenary discussion with trans‐disciplinary experts regarding Lake Victoria fisheries research, management and policy sectors, the present study identified current management challenges, gaps and priorities. The present study results indicate a constantly increasing fishing effort, poor enforcement of existing regulations and pollution and invasive weeds pose the greatest threats to the sustainability of Lake Victoria's fisheries resources. Policy gaps include a lack of regulations on emerging technologies (e.g. cage culture) and an absence of implementation guidelines and framework for some existing policies. The aspects and gaps of each challenge are discussed, using available literature for the lake, with policy and capacity interventions recommended under each section for sustainable management of Lake Victoria fisheries resources.