Lake Victoria in East Africa is the world's second largest freshwater system. Over the past century the ecosystem has undergone drastic changes. Some 30 years after the introduction of Nile perch (Lates niloticus) and Nile tilapia (Oreochromis niloticus) in the 1950s, the highly diverse community of native haplochromines collapsed, leaving a system dominated by only four species: the native cyprinid dagaa (Rastrineobola argentea) and shrimp (Caridina nilotica), as well as the introduced Nile perch and Nile tilapia. More recently, an unexpected resurgence of haplochromines has been reported. To understand these changes in terms of ecosystem functioning and of changes in growth of trophic groups, we created mass balances of the food web near Mwanza, Tanzania, before, during, and after the Nile perch boom (1977, 1987, and 2005), using the application ECOPATH. We connected these mass balances with a dynamic model assuming linear trends in net growth rates of the trophic groups. Our analysis suggests that the Nile perch boom initially altered the biomass distribution over trophic levels. Also, results indicate that not only fishing but also changes at the detritivores' trophic level might have played an important role in driving changes in the system. Both the mass balances and the dynamic model connecting them reveal that, after a major distortion during the Nile perch boom, the biomass distribution over the main trophic levels had largely recovered its original (1977) state by 2005. However, no such return appeared in terms of community structure. Biodiversity in the new state is dramatically lower, consisting of introduced species and a few native surviving species. We conclude that at an aggregate level Lake Victoria's ecosystem has proved to be resilient in the sense that its overall trophic structure has apparently recovered after a major perturbation. By contrast, its intricate functional structure and associated biodiversity have proved to be fragile and seem unlikely to recover.