The purpose of this study is to determine the factors responsible for the prevalence of urinary stones disease among the inhabitants of selected regions in northern Jordan and to trace the extent of their link with the hydrogeochemical properties of groundwater in the area in addition to geoenvironmental factors and some certain dietary habits. By comparing the disease spread in the studied areas, results showed that the elevated areas (Irbid and Amman) are the most affected regions with the disease. One hundred and thirty water samples collected from 15 wells were distributed across the three studied regions to identify urinary stone patients among individuals. All samples were analyzed for percentages of cations and anions to assess water quality. Anions are distributed in the following order: HCO3− >Cl− >SO42− >NO3− >F− >PO43−, while the cations are distributed as follows: Ca2+ >Mg2+ >Na+ >K+ >Fe2+. The hydrogeochemical analysis results for the three regions compared using the Wilcoxon rank-sum test. The significant difference in the values of TDS, TH, Cl−, NO3−, Ca2+, and Mg2+ is p < 0.05 compared with water quality in the regions of Amman–Mafraq and Irbid–Mafraq. Depending on Gibbs’ diagram and the factor analysis, elements ratio plots strongly suggest that the source of chemical ions in the groundwater is the interaction of water with carbonate rocks. Therefore, this study confirms the strong relationship between urinary stones formation and the geochemistry of drinking water during the high calcium content and increase of the water hardness used by the residents of the study areas. The effect of temperature on the formation of urinary stones was observed through the direct correlation with the amount of water consumed by individuals. In winter, the daily water intake decreases, which leads to an increase in the concentration of Ca, Na, and P ions in the bladder. The high temperature in the summer increases the dehydration process in the body, which increases the concentration of calcium and other ions to create an opportunity for urine stones to form.