A systematic study has been carried out to assess the water quality index of river Pazhayar in kanyakumari district. The pH of the water samples from three stations varied from 6.8 in winter to maximum of 8.70 in summer. The total dissolved solids of the river water samples analysed during monsoon-I varied 11.00mg/l at Manakudy (St-III), in winter season to maximum 910.0 mg/l at Manakudy (St-III) in summer season. The temperature, pH, total dissolved solid, total alkalinity, total hardness, calcium, magnesium, sodium, potassium, chloride, Dissolved oxygen were also studied at different station in different season. Bacterial populations in different stations were studied in Pazhayar River of Kanyakumari District, Tamil Nadu. Bacterial Population in river water showed a minimum of 32×10־³CFU (colony forming unit) in station - I during summer to a maximum of 198×10־³CFU in station – II during summer season.The statistical analyses reveals the dependency of physico chemical and biological factors. Correlation coefficient for bacterial population were compared with variables showed positive and negative correlation at 0.01 and 0.05 level of significant. The quality of water was found to be determined by the environmental conditions, physiochemical parameters, biological factors and the anthropogenic activity.