Recently, toxins and off-flavor compounds produced by phytoplankton in freshwater ponds have become a concern as it affects consumer acceptability and food safety. The purpose of this research was to investigate the relationship between phytoplankton abundance and water-sediment physicochemical parameters in high-nutrient-load Nile tilapia (Oreochromis niloticus) ponds from three sub-districts (upazila) in north-central Bangladesh. Water and sediment samples were collected from 9 randomly selected ponds of Sadar, Trishal, and Muktagachha upazila, and temperature, transparency, pH, phytoplankton concentration for water and pH, organic C and organic matter for sediment samples were determined. Water temperature and transparency were more or less similar across all the ponds, while pH varied significantly (p<0.05). Soil pH also varied significantly (p<0.05). The abundance of Bacillariophyceae, Chlorophyceae, and Euglenophyceae in pond water was almost equal but Cyanophyceae differed among the ponds with the highest in Muktagachha (5.22±2.30×104 cells/L) and the lowest in Trishal (4.84±0.740×104 cells/L). Correspondingly, Algal Genus Pollution Index (AGPI) was employed to study the water quality of Nile tilapia ponds, and it revealed that ponds in Muktagaccha had ‘probable high organic pollution’ compared to ponds in the other two locations. Five cyanobacteria genera were identified viz., Anabaena, Aphanizominon, Gomphosphaeria, Mycrocystis and Osoillatoria where Anabaena showed a strong positive correlation with water temperature and pH. The significantly higher abundance of cyanobacteria in Muktagachha is possibly linked to the favorable water temperature and pH and indicates a higher risk of off-flavor creation in the Nile tilapia ponds from this upazila. It is, therefore suggested that the right management measures must be put in place to control the cyanobacteria to ensure the profitability of fish farming.