Ichthyofaunal diversity and the impact of anthropogenic activities on fish population assemblages were studied in Lake Cayo, a small lake located in the coastal region of the Republic of Congo. Twelve stations were sampled twice over a two-year period. Fishing techniques following standardized methods utilizing monofilament gill nets, and nine environment variables were measured at each station. A total of 11,361 specimens comprising 30 species in 28 genera and 18 families were collected with the Cichlidae being the most diversified. Redundancy Analysis with forward selection coupled with Monte Carlo permutation tests identified depth, pH and substrate as accounting for 57.7% of the total variance among the nine variables sampled (p < 0.05). The low Shannon’s diversity (1.16 ± 0.33) and Equitability (0.43 ± 0.12) indices at all sites, suggest that the Lake Cayo system is in poor ecological health.