The objective of this study was to examine the relationship between calcium (Ca) and magnesium (Mg) in underground water (UGW), bottled mineral water (BMW), and domestic treated water (DTW) with related to risk of kidney stones. The water samples were collected from different areas of Sindh, Pakistan. The scalp hair samples of both genders, age ranged 30-60 years, consuming different types of water, have or have not kidney disorders, were selected. The Ca and Mg concentrations were determined in scalp hair of study subjects and water by flame atomic absorption spectroscopy. The Ca and Mg contents in different types of drinking water, UGW, DTW, and BMW, were found in the range of 79.1-466, 23.7-140, and 45-270 mg/L and 4.43-125, 5.23-39.6, and 7.16-51.3 mg/L, respectively. It was observed that Ca concentration in the scalp hair samples of kidney stone patients consuming different types of drinking water was found to be higher (2,895-4721 μg/g) while Mg level (84.3-101 μg/g) was lower as compare to referents subjects (2,490-2,730 μg/g for Ca, 107-128 μg/g for Mg) in both genders. The positive correlation was found between Ca and Mg levels in water with related to kidney stone formations in population, especially who consumed underground water. A relative risk and odd ratio were calculated; the relative risk had a strong positive association with incidence of kidney stone which depends on types of drinking water.