ABSTRACT The present study aims to evaluate the distribution of organochlorine pesticides in the Loktak Lake and its draining rivers over a spatial and seasonal scale. Organochlorine pesticides including α- HCH, β- HCH, γ- HCH, δ- HCH, Aldrin, 4,4-DDE, Endrin, Endosulfan II, 4,4-DDD, Endrin Aldehyde, Endosulfan sulphate and 4,4-DDT were analysed in the water and sediments adopting gas chromatography and mass spectrometric techniques. The concentration of pesticides recorded the highest concentration of 2271 ng/l in the water samples and 5319 ng/g in sediment samples. In water samples, Endosulfan II, Endrin and γ- HCH were present at the higher concentrations, whereas α-BHC was recorded at the lowest at 0.78 ng/l. In sediment samples, 4, 4-DDT recorded the highest concentration, followed by 4,4-DDD and Endosulfan II. Human health risk assessment based on water consumption shows higher risk potential from five pesticides. Pesticides in the region may pose a threat to the wetland comprising vital flora and fauna of the biodiversity hotspot. The bacterial population was more or less related to the pesticide concentration, with a lower population at less contaminated sites.