Subsurface water is a vital resource in arid environments. This study investigated spatiotemporal differences in heavy metal concentrations and associated health risks with subsurface water in various parts of Bikaner City, Rajasthan, India. Eighty subsurface water samples were collected from 20 locations in the pre-monsoon and monsoon seasons and analyzed for arsenic (As), chromium (Cr), copper (Cu), manganese (Mn), lead (Pb), uranium (U), and zinc (Zn). Contamination was assessed using multiple indices, including the contamination factor (CF), degree of contamination (C-d), modified degree of contamination (mC(d)), geo-accumulation index (I-geo), pollution load index (PLI), potential ecological risk index (PERI), heavy metal pollution index (HPI), metal index (MI), carcinogenic risk index (CRI), and hazard quotient (HQ) . Pb and U were determined to be the most concerning pollutants, especially during monsoon season. The sampling locations of Raisar and Khara appear to be contaminant hotspots. Metal health risk assessment indicates that hazard index (HI) of more than 1 was found in As, Cr, Cu, Pb, and U. Lead had maximum HI followed by U in both children and adults. Chromium and Pb were cancerous metals present in subsurface waters. Total cancer risks (TCRs) during the pre-monsoon and monsoon seasons were above permissible limits. Future work should include a larger number of samples and further assess potential contamination sources.