A user-friendly software model, Ecopath with Ecosim, version 5.0 Beta, was used to construct energy flow and mixed trophic impact (MTI) for the Lake Awassa ecosystem (Ethiopia). We used data from the literature and also several parameters were estimated from the present study done from November 2003–August 2004. Thirteen functional groups including two ontogeny ones were used in the present analysis, which assessed the trophic relationship, energy flow and interactions between them. The producers particularly phytoplankton and detritus are under exploited; hence energy transfer from lower trophic levels is low. On the contrary, all consumers have ecotrophic efficiency (EE) close to 1 indicating that consumers are heavily exploited in the system. Flow from detritus was as important as flow from phytoplankton. Flow from both herbivorous and carnivorous zooplankton to consumers was high. MTI analyses indicate that phytoplankton and detritus have positive impact on most other groups while zoobenthos has negative impact on some groups. Lake Awassa has low ecological efficiency with a value of 0.00144 for the gross efficiency of the fisheries. The system primary production/respiration (P/R) ratio of Lake Awassa is 5.834 showing that the lake is at developmental stage, with high autotrophy, and some attention should be given to human impacts. This trophic model analysis also enabled us to confirm/refute previous studies and pinpoint critical gaps in the present knowledge about Lake Awassa.