The East African Rift System defines the setting of most of Kenya's important internal (e.g., Lakes Nakuru, Naivasha, Baringo, Bogoria) and transboundary (e.g., Lakes Turkana, Victoria) lake basins. The lakes support ecosystems that are rich in birdlife, wildlife and aquatic macrophyte species, but the influent rivers have low species diversity. The lakes and rivers are valuable to the area inhabitants as they provide water and food for humans and livestock, food and nutrition from fisheries, materials for building and weaving, tourism and recreational services, and have aesthetic values. The lakes are, however, experiencing changing trophic status, and this is largely due to increased and in many cases unsustainable human activities within their catchments, including deforestation, large scale damming, excessive surface and ground water abstraction, pollution from agriculture and industries, siltation, livestock pressure and increased intensity of human exploitation of the resources. Some of the governance and management challenges that are recognised include: absence of institutional structures in some cases; differentiated capacities to manage the basins; inadequate or ineffective decision-support tools; inadequate levels of transboundary coordination; and_low and uncoordinated participation by stakeholders. This research explores these governance and management challenges using Kenya's internal and transboundary lakes as a case study, and examines how the Integrated Lake Basin Management (ILBM) conceptual framework, with its six fundamental pillars for governance improvement (institutions, policies, participation, technology, information, and finance) can be brought to bear to ensure sustainability of the lakes and their supporting natural and built infrastructure in the context of balancing conservation and development.