The long-term sustainability of the African Great Lakes is strongly connected to the management and monitoring of their coastal areas. Yet, the communities that live in these areas are rarely involved in monitoring and have limited influence on key management issues. Furthermore, regulatory activities and knowledge sharing in these transnational ecosystems are strongly limited by funding and infrastructure limitations. Citizen science has great potential to advance both scientific and public understanding of the state of the environment. However, there remains a limited understanding of participants’ motivations and expectations, especially in developing countries, where citizen science has great potential to complement regulatory monitoring. The present study explores the motivations of citizen scientists in villages along Lake Tanganyika’s northern coast and their potential to take a more active role in lake management. Motivations were examined through qualitative interviews, focus groups, and quantitative surveys with 110 citizen scientists and 110 non-citizen scientists from participating villages. Key motivational factors identified were the desire to contribute to scientific research and local knowledge, as well as aspects of financial compensation. The results confirm that participation in citizen science provides many benefits to participants beyond their role as data aggregators and final knowledge users. However, the incentives to participation varied to those typically considered in citizen science programs conducted in developed countries. To create sustainable long-term community based environmental monitoring, these motivations should be incorporated in the program design and participant recruitment.