Ecosystem-based fisheries management (EBFM) is an important complement to existing fisheries management approaches to maintain ecosystem health and function; to translate goals and aspirations for sustainability into operational objectives, the preferences of the fishing communities should be considered for successful implementation of EBFM. This study analysed the preferences of the fishing community for alternative EBFM developments for Lake Naivasha, Kenya, and estimated the willingness to pay, using a choice experiment approach.