In order to compare the magnitudes and health impacts of arsenic and other toxic trace elements in well water, groundwater and hair samples were collected from three areas with different arsenic exposure scenarios in the Mekong River basin of Cambodia. Ampil commune in Kampong Cham province was selected as an uncontaminated area, Khsarch Andaet commune in Kratie province was selected as a moderately contaminated area, and Kampong Kong commune in Kandal Province was selected as an extremely contaminated area. Results of ICP-MS analyses of the groundwater samples revealed that As, Mn, Fe and Ba concentrations were significantly different among the three study areas (Kruskal-Wallis test, p < 0.0001). Out of 46 observed wells in the Kandal province study area, 100% detected As > 50 μg L(-1) and Fe > 300 μg L(-1); 52.17% had Mn > 400 μg L(-1) and 73.91% found Ba > 700 μg L(-1). In the Kratie province study area (n = 12), 25% of wells showed elevated arsenic levels above 10 μg L(-1) and 25% had Mn > 400 μg L(-1), whereas samples from Kampong Cham province study area (n = 18) were relatively clean, with As < 10 μg L(-1). A health risk assessment model derived from the USEPA was applied to calculate individual risks resulting from drinking groundwater. Computational results indicated that residents from Kandal Province study area (n = 297) confronted significantly higher non-carcinogenic and carcinogenic risks than those in Kratie (n = 89) and Kampong Cham (n = 184) province study areas (Kruskal-Wallis test, p < 0.0001). 98.65% of respondents from the Kandal province study area were at risk for the potential non-cancer effect and an average cancer risk index was found to be 5 in 1000 exposure. The calculations also indicated that, in the Kratie province study area, 13.48% of respondents were affected by non-cancer health risks and 33.71% were threatened by cancer, whereas none of respondents in the Kampong Cham province study area appeared to have non-carcinogenic effect. Positively significant correlations of the arsenic content in scalp hair (As(h)) with both arsenic levels in groundwater (As(w)) (r(s) (304) = 0.757, p < 0.0001) and individual average daily doses (ADD) of arsenic (r(s) (304) = 0.763, p < 0.0001) undoubtedly indicated that arsenic accumulation in the bodies of Cambodia residents in the Mekong River basin was mainly through a groundwater drinking pathway. To the best of our knowledge, this is the first comprehensive report comparing individual health risk assessments of arsenic exposure through a groundwater drinking pathway to enriched arsenic levels from groundwater in the Mekong River basin, Cambodia. This study indicates that elevated arsenic concentrations in groundwater may lead to thousands of cases of arsenicosis in the near future if mitigating actions are not taken.