Background and Objective: Cultivating fish in a controlled environment has been found to expose them to contamination by microorganisms (pathogenic and opportunistic organisms). This contamination is attributed to questionable water quality and high stocking densities. Inability to change the water in ponds exposes the fish to microbial agents which when encountered, cause diseases and death. The microbiological and physicochemical qualities of some fish ponds water at MOUAU, Umudike alongside a reservoir that supplies the water at NRCRI, Umudike were measured out. Materials and Methods: The microorganisms were identified with biochemical tests and molecular techniques using PCR and DNA sequencing. The physicochemical parameters were assessed using appropriate methodologies. The fungi isolates were identified based on colony features and microscopic examination of mounts of the isolate made in lactophenol blue. Results: The total heterotrophic bacteria mean count ranged from 5.6×10 6 ±1.41 in the reservoir to 1.56×10 7 ±1.41 in pond 3. Similarly, the fungal count ranged from 1.8×10 6 ±0.14 in the reservoir to 3.8×10 5 ±0.14 in pond 5. The bacteria isolated were Alcaligenes faecalis (16.9%), Salmonella bongori (13.8%), Staphylococcus sciuri (18.5%), Proteus mirabilis (15.4%), Pseudomonas aeruginosa (24.6%), Escherichia coli (10.8%), while the fungi were Aspergillus niger (36.4%), Aspergillus fumigatus (27.3%), Penicillium glabrum (24.2%) and Rhizopus oryzae (12.1%). The mean values of the physicochemical parameters ranged as follows: