This article focuses on the temporal and spatial distribution of three organophosphorous pesticides-malathion, methyl parathion, and chlorpyrifos-in the sedimentary environment of a backwater ecosystem, Kuttanad backwaters, situated in Kerala, India. Based on salinity distribution, geographic characteristics, and human activities prevailing in the area, the study area was divided into three zones: zone 1 with riverine characteristics, zone 2 with freshwater characteristics during and after the monsoon season and estuarine characteristics during the premonsoon season, and zone 3 with estuarine characteristics. The organophosphorus pesticides in the study area showed the order of enrichment as chlorpyrifos >malathion >methyl parathion. While studying the variations in pesticide concentrations seasonally, higher concentrations were observed during the premonsoon monsoon season, with the concentrations being lower than the detectable level. Sediment characteristics, such as pH, texture, organic carbon, moisture content, etc., had reflective effect on the degradation rates of pesticides. The runoff water from the paddy fields made a larger contribution of pesticide pollution to the study area.