Using isotopes to determine the natural and anthropogenic processes influencing water quality in household wells of Chronic kidney disease of unknown origin (CKDu) endemic Medawachchiya area, Sri Lanka

•Environmental isotopes used to advance hydrological studies in CKDu endemic areas.•Nutrient cycling in domestic well water identified by using C & N isotopes of POM.•Rock water interactions control the chemistry of well waters in Medawachchciya.•Novel integrated approach of hydrochemistry, environmental isotopes & POM characteristics.•Approach allows differentiation between natural and anthropogenic solute sources. The groundwater in the dry climatic, agricultural regions of Sri Lanka has been a focus of research for more than two decades as a likely contributor to the epidemic chronic kidney disease that does not have an identified causality (CKDu). The intense agriculture that heavily depends on irrigation and excessive use of agrochemicals, as well as the increasing population that prompt over-extraction and sewage discharge presents increasing threats to these groundwaters. Particulate organic matter (POM), stable environmental isotopes (13C, 15N, 18O and 2H) together with hydrochemistry were used to determine the natural and anthropogenic sources of solutes, and their dynamics in these waters. Twenty nine domestic drinking water wells and spring were sampled from CKDu endemic Medawachchiya area during the dry season of 2018. POM of most waters were found to have aquatic origin resulted from biological processes that assimilate nutrients in groundwater. The isotopic compositions (18O and 15N) of nitrate provided evidence for anthropogenic nitrate inputs in some wells and denitrification of potentially anthropogenic nitrates in others. These waters were recharged locally and subjected to varying degrees of evaporation. The water–rock interactions, evaporation, and anthropogenic inputs significantly influence shallow drinking water quality in wells (