Man-made lakes are alternative and potential habitats for biodiversity conservation, fisheries and extensive aquaculture. We investigated the ecology and the fish community structure of two (2) sand-dragged man-made lakes, Lake Ahozon and Lake Bewacodji of Southern Benin, with implications for species conservation, fisheries management and aquaculture valorization. From August 2014 to July 2015, habitats conditions were evaluated and fishes were sampled monthly with seine, cast net, experimental gill net and hooks in the open water and aquatic vegetation habitats of both lakes. Overall, the water quality of Lake Ahozon was globally favorable for the growth and the survival of the fish resources whereas Lake Bewacodji exhibited a poor water quality indicated mainly by an acid pH (mean: 6.32 ± 0.58) and low dissolved oxygen concentrations (mean: 3.52 ± 1.25 mg/l) caused by dense floating plants, Nymphea sp mainly and huge daily dumping of domestic wastes. The study revealed low species richness, d = 5.89 and d = 3.87, and low species diversity, H’ = 0.76 and H’ = 0.48 for Lakes Ahozon and Bewacodji, respectively, with Lake Ahozon more diverse than Lake Bewacodji. The fish community of Lake Ahozon comprised six (6) species, 3 cichlids Sarotherodon galilaeus, Oreochromis niloticus and Tilapia guineensis, the silver catfish, Chrysichthys nigrodigitatus (Claroteidae), the African bonytongue, Heterotis niloticus (Osteoglossidae), and the African catfish, Clarias gariepinus (Clariidae). Numerically, S. galilaeus dominated Lake Ahozon and made 85.21% of the sample. In Lake Bewacodji, the fish composition comprised four (4) species, Sarotherodon galilaeus multifasciatus, the dominant species making numerically 91.58% of the total sample, T. guineensis, C. gariepinus and C. nigrodigitatus. With regard to trophic structure, the fish assemblages of both lakes were numerically dominated by planktinovores/ detritivores, mainly S. galilaeus, O. niloticus, T. guineensis and C. nigrodigitatus making together 99.46% of Lake Ahozon fish community, and S. galilaeus multifasciatus, T. guineensis and C. nigrodigitatus accounting together for about 98.59% of Lake Bewacodji. In Lake Ahozon, standard length (SL) frequencies histograms showed an unimodal size distribution for H. niloticus, the nile tilapia O. niloticus and C. gariepinus whereas the two cichlids, S. galilaeus and T. guineensis exhibited a bimodal size distribution. In Lake Bewacodji, S. galilaeus multifasciatus, C. nigrodigitatus and C. gariepinus exhibited an unimodal size distribution. A sustainable exploitation of both man-made lakes requires the implementation of an integrated management scheme which should include habitat restoration and protection plan, fisheries/aquacultural valorization, ecological sound agriculture/ecotourism and environmental monitoring.