Two freshwater fish samples (Claries gariepinus and Oreochromis niloticus) were harvested from two different locations (MOUAU and Umugbalu fish farm). The fish samples were treated in constructed small scale depuration system. Bacterial quality of the fish samples, its habitat and UV treated water used for fish treatment during depuration were also investigated. Similarly, the physicochemical properties (pH, temperature, salinity, turbidity and dissolve oxygen) of the habitat (pond) were investigated. Furthermore, the initial fish weight before and after depuration were analyzed. The total plate count of the fish samples were determine and isolates characterized before and after depuration.