The diversity of bacteria in freshwater is influenced by some important physicochemical factors and autotrophic nutrients. Their diversity can be employed as a sensitive pollution indicator in the environment and change because bacteria respond quickly to changes in the ecosystem. Analysis of physicochemical and bacteriological quality of humic freshwater and sediment was carried out on samples from three (3) geo-referenced sections of Eniong River, AkwaIbom State designated ST3 (Upstream), ST2 (Midstream) and ST1 (Downstream) using standard analytical methods. The results obtained were compared with World Health Organization (WHO) and Federal Ministry of Environment (FMENV) standards. The study revealed that thesamples had a mean heterotrophic bacterial count of 5.95±0.41 log10 CFU/g and heavy pollution with faecal bacteria such as (4.31±2.51 log10CFU/g TCC and 5.19 ±0.33 log10CFU/g FCC), including mean counts of Staphylococcus spp (5.90±1.16log10CFU/g), Vibrio spp (.21±1.04 log10CFU/g), Salmonella-Shigella (3.15±0.33 log10CFU/g), and Actinomycetes (3.29±2.49 log10CFU/g) that considerably exceeded the recommended range of WHO/FMENV for portability. The most abundance bacteria in were Bacillus subtilis, S. aureus and Shigella spp (55.6%) followed by Pseudomonas aeruginosa, Bacillus subtilis, Salmonella, Nocardia sp, Proteus sp., Staphylococcu sspp, Burkholderia pseudomallei and Enterococcus faecalis with a prevalence rate of 44.4%. The results showed the mean DO (7.67±0.037 mg/ml)), EC (85.07±0.52 μS/cm) and temperature (27.480C±0.049) of Eniong river water were within acceptable standard values while TSS (12.5 mg/ml) and TDS (19.0±1.30 mg/ml) values were not. Also, Pb, Cd, Vn, Ni and Cu recorded higher values while the concentrations of Fe2+, K+, Na+, Ca2+ and Mg2+ were remarkably low in both water and sediment. The mean pH of the river and sediment were 6.48±0.018 and 6.42±0.019, respectively. Similarly, among the anionic surfactant, the mean values for nitrate, carbonate and sulphate were higher in sediment than in water, while carbonate was not detected in water. The findings imply that the quality of Eniong River water and sediment is heavily compromised. Therefore, the creation of awareness on the importance of water safety and hygiene, regular monitoring of drinking water quality and enforcement of compliance with the standards by regulatory agencies are recommended to eschew possible health hazards.