Nonpoint source pollution from agricultural runoff which contains hazardous agrochemicals like pesticides and fertilizers threatens water bodies, posing a serious danger to aquatic ecosystems and drinking water resources. Use of agrochemicals in rice cultivation has rapidly increased in the last few decades in Sri Lanka. It has been reported that many agrochemicals contain toxic trace elements like As, Cd, Pb, Zn, Cu, Ni, Cr, Al, etc. To reduce the harmful effect of heavy metal contain-ing agrochemicals, the Government of Sri Lanka has banned the use of several toxic agrochemicals in recent years. In this context, this study was conducted after posing these restrictions to assess the occurrence of heavy metals in surface water bodies in rice cultivation areas in Trincomalee district, Sri Lanka. Ninety-three (n = 93) sample locations were randomly selected for collection of water, before and after applying agrochemicals to rice fields. This include areas from rural farm-ing communities having endemic (Padavi Sripura DS) and non-endemic (Kanthala DS and Seruvila DS) Chronic Kidney Disease of unknown etiology (CKDu). Mean and standard error of mean of As, Cd, Pb, Cu and Zn concentrations (µg/L) before and after applying agrochemicals were as {0.048 ± 0.038 and 6.220 ± 0.912}, {0.014 ± 0.013 and 0.371 ± 0.192}, {not detected and 4.421 ± 0.712}, {1.583 ± 0.397 and 1.262 ± 0.165} and {not detected and 6.403 ± 0.366}, respectively. Findings revealed that concentrations of As, Cd, Pb and Zn were significantly different (p < 0.001) before and after the application of agrochemicals. However, the observed heavy metal concentrations were far below the permissible levels for irrigation water set by Food and Agriculture Organization and United States Environmental Protection Agency, ambient water quality set by Central Environmental Authority, and drinking water quality set by World Health Organization. In addition, analyzed heavy metal concentrations in surface water samples from CKDu endemic areas were not significantly different from those from non-endemic areas (p < 0.05). To our knowledge, this is the first report of heavy metal analysis after government ban of agrochemicals. Therefore, continuous detailed research is required to fully comprehend the behavior of agrochemicals in surface water bodies in Sri Lanka.