The proliferation of chronic kidney disease of unknown etiology (CKDu) in Sri Lanka may be attributed to exposure to trace elements of both natural and human origin in the environment, which has been extensively explored and widely debated within the scientific community. This research aims to investigate the fluctuation of soil quality in paddy fields concerning depth and to evaluate the corresponding groundwater parameters in a region identified as a high-risk area for CKDu in the North Central region via determining different parameters including trace metals in both paddy soils and groundwater. The slightly alkaline paddy soils in the study area displayed elevated electrical conductivity values in the uppermost soil layer compared to the subsoil layer. Although hazardous metals, including lead (Pb), chromium (Cr), arsenic (As), and cadmium (Cd), were detected in the paddy soil, they did not surpass the critical toxic concentrations. A statistically remarkable robust positive correlation was discovered between the concentration of Pb in the soil and its depth. Additionally, the levels of toxic metals, such as lead, arsenic, cadmium, and chromium, in the study area’s groundwater were substantially lower than the safety standards set by the World Health Organization. However, some groundwater samples were found to contain anionic species, including fluoride, in concentrations that exceeded the established permissible limits. The gradual accretion of trace elements within the paddy soil presents a potential hazard for the translocation of such elements into the rice plants, thus constituting a possible threat to human health.