Levels of regional endemism are notably high with 82% of fish and 74% of molluscs restricted to the region. Species diversity is also high and the major centres of diversity are the African Great Lakes of Malawi/Nyassa/Niassa, Tanganyika and Victoria, and in the Eastern Arc Mountain Range (for Odonata).

Major threats are identified as loss and degradation of habitat, in particular from sedimentation due to deforestation and eutrophication, and the introduction of alien species. The centres of threatened species are the African Great Lakes and a number of East Coast river drainages. A major concern for the future is the potential impact of water resource developments such as for improved water supply, irrigation and provision of hydroelectric power.

A gaps analysis found that inland waters are poorly protected within the existing Protected Areas network which is largely focused on terrestrial ecosystems. Forest Reserves were, however, observed to provide effective protection of watersheds at the headwaters of some river systems; it is recommended that their legal status be raised to provide a greater incentive for their effective management and for increasing the potential for attracting funds.

Finally, it is most important that the data from this study are made available to the relevant decision makers and stakeholders in a format that can be easily understood and readily integrated within the decision making process. With this in mind, this work has been extended to the rest of Africa and a series of "Good Practice Guidelines" are being developed at four sites, one of which is the Rusizi Delta in Eastern Africa.