In many parts of Africa, human populations depend directly or indirectly on rivers and wetlands. Despite this importance, basic ecological aspects of most aquatic communities are still poorly understood and destructive activities such as deforestation and dam construction are in rapid ascent, threatening waterways and their wetlands. It is therefore crucial to improve our understanding on the ecology of these areas, so that the responses of aquatic communities to the different alterations to the natural environment can be predicted and impacts mitigated. This study will investigate the main sources of nutrition and the patterns of food web structure in (sub)tropical East African systems. The specific objectives are: 1) to understand the importance of imported (terrestrial) material for animal communities in freshwater and estuarine systems of (sub)tropical East Africa, 2) describe the food web organisation in these areas, 3) identify trophic processes characteristic of these food webs that can be used as indicators of ecosystem health and 4) determine the main environmental factors regulating the flow of material in these areas. The study will be based on stable isotope analysis and will focus mostly on macroinvertebrates and fish. Three large East African rivers, the Tana (Kenya), Zambezi (Mozambique) and the Betsiboka (Madagascar) will be sampled, along with six artificial reservoirs and two large lakes in Ethiopia. In each system, sites with different environmental conditions and subjected to different impacts will be considered, to multiply the potential to detect general patterns and successfully attribute causalities. Novel techniques to the treatment of stable isotope data will be applied and further developed to maximize the information extracted from the data. Environmental settings such as topography, river-flow and adjacent land use will also be considered, so that results can be linked to differences in environmental conditions, and types of impact.