Freshwater bodies of Akwa Ibom State North-West District, Nigeria, were studied between May and December 2021 at seven sampling stations based on human activities. The indices used were water quality index (WQI) for drinking water purpose, comprehensive pollution index (CPI) for aquatic life sustainability, and Palmer pollution index (PPI) for organic pollution. Thirteen physicochemical parameters were scrutinized using standard methods and compared with the World Health Organization (WHO) standards. All the physicochemical parameters evaluated were within the acceptable limits, except pH, biochemical oxygen demand (BOD), dissolved oxygen (DO), and nitrate in some stations. The phytoplankton identified comprised13 genera of pollution indicators out of 41 genera of the total population, among which Bacillariophyceae accounted for 46.55%. The WQI values ranged between 38.86 and 54.63 based on weighted arithmetic method. The CPI values ranged from 0.35 to 0.46, while the PPI score ranged between 1 and 23. The values of WQI and CPI obtained in stations I, III, and IV revealed poor water quality which was unfit for human consumption and sustenance of aquatic life. The obtained value for PPI revealed that stations I, III, IV, VI, and VII were organically polluted. The occurrence of pollution indicator genera in these stations further proved that the water bodies were moderately polluted owing to anthropogenic perturbation. The activities of humans within the watershed should be of concern to the relevant authorities; regulation of these activities should be enforced to minimize the situation of water deterioration and for regaining the natural water quality to support aquatic life and health and make it fit for domestic usage.