Abstract: Background and Objective: Limnological information of Kainji Lake is key in the development and management of the lake. Kainji Lake receives organic and inorganic wastes through animal husbandry operations, illegal mining activities, washing, bathing, direct waste disposal and other human activities. The objective of this research is to evaluate the limnological qualities of water from southern basin of the lake. Materials and Methods: Determination of faecal coliform (an indicator of biological pollutants) was carried out. Bacterial identification was also determined using primary isolation media and microbat identification kits, 12A and 12B (MB1132A/Australia). The concentration of lead (Pb), copper (Cu), cadmium (Cd), chromium (Cr), arsenic (As) and physicochemical parameters such as dissolved oxygen (DO), Biological Oxygen Demand (BOD), temperature, transparency, pH, conductivity, Total Alkalinity (TA), Total Dissolved Solids (TDS), nitrate and phosphate were determined. Results: Mean faecal coliform count in all the sampling stations were observed to be below the maximum permissible limit of 1.0×103 MPN/100 mL according to WHO. Faecal coliform counts during the wet season were higher than that during the dry season. Bacterial pathogens were identified. Physicochemical parameters were observed to be within an acceptable range for aquatic lives. Copper and arsenic were observed to be within the acceptable limit. Concentrations of cadmium in all sampling stations were above the maximum permissible limit. Conclusion: Faecal coliform count and physicochemical parameters are within favorable range for aquatic lives; however there was the presence of pathogens. Cadmium (Cd) in all sampling stations was above the maximum permissible limit.