Biodiversity within inland water ecosystems in Eastern Africa is both highly diverse and of great regional importance to livelihoods and economies. However, development activities are not always compatible with the conservation of this diversity and it is poorly represented in the development planning process. This document provides the background, assessment methodology, results, and conclusions and discussions on the IUCN/SSC Freshwater Biodiversity Assessment Programme, which aimed to eliminate the information bottleneck for effective biodiversity conservation and livelihood protection in the inland waters of Eastern Africa.