Fossil fish remains from Gona, Ethiopia, were recovered along with those of other vertebrates by the Gona Paleoanthropological Research Project team (GPRP) in the late 1990s and early 2000s from Pliocene and Pleistocene deposits. The early Pliocene fish were recovered from natural depositional contexts, whereas the early Pleistocene fish were associated almost completely with archeological contexts. Analysis of the fossils provides new information on the Pliocene and Pleistocene fish taxa from deposits associated with the Awash River system in the Afar Depression, Ethiopia. Six families are represented in the fossil assemblages, including one not previously reported from the Pliocene Awash River system. Based on the methodology of a previous study, we test the accuracy of using habitat preferences of modern fish taxa to infer the preferences of the same fossil taxon. Our findings contribute to the reconstruction of the paleoecology of the Pliocene Awash river and lakes. The presence of several hyperostotic cichlid bones in both the Gona and Middle Awash project areas indicates that periods of stability in the lakes and rivers of the Awash River system were punctuated by occasional periods of extreme changes in water levels and water chemistry, resulting in intense soda conditions, which would eradicate most fish taxa. Fish bones recovered from the localities with archeological contexts differed in taxonomic composition and diversity from the naturally deposited assemblages, suggesting the possibility that these remains were selected and accumulated by humans.