The Gilgel Gibe Reservoir is at risk of eutrophication by the inefficient use of fertilizers, the important animal waste disposal, together with the high soil erosion, and the discharge of liquid and solid waste from the populations upstream the reservoir. Our study aimed to (1) understand the aquatic food web structure of the dam and create an ecosystem state baseline in case of future deterioration and (2) to evaluate the impact of nitrate pollution by Jimma city on the Gilgel Gibe River waters, which feed the Gilgel Gibe Reservoir. Reservoir Food Web Study Fish, plankton, sediments, benthic macroinvertebrates, macrophytes, periphyton and terrestrial leaves were analyzed for stable isotopes of nitrogen (d¹5N) and carbon (d¹³C) to study the food web structure at Gilgel Gibe Reservoir and to understand the main food sources of the two fish species present at the dam, Labeobarbus intermedius and Oreochromis niloticus. Our isotope data revealed that L.. intermedius most likely feeds on macrophytes, scraper macroinvertebrates and zooplankton. O. niloticus ¹5N and d¹³C values revealed a missing component in our food web analyses. We hypothesized a cannibalism behavior between early life stages, which will constitute the missing component at our food web. Nitrate Fate and Sources Study A dual isotope approach (d¹8O-NO3? and d¹5N-NO3?) was used to trace the source and fate of the nitrates present at the surface waters of the city of Jimma, Boye Wetland and the Gilgel Gibe River. Overall, our study did not reveal an important contribution of urban and wetland nitrate towards the Gilgel Gibe River waters. We assume that the natural treatment function of the wetland removes all nitrate coming from the city. However, considering the increasing industrial activities and population densities in the area and the lack of a waste water treatment system in the city, a most likely future scenario includes a saturation of the natural wetland treatment capacity and a subsequent contamination of the Gilgel Gibe waters by nutrients coming from the city. Management priorities should focus on improving the sewer collection system, incorporating some treatment for this water and a periodical monitoring of the wetland N-species concentrations in order to identify saturation of the Boye Wetland natural treatment functions.