Natural and anthropogenic factors highly influence the concentration of major (Na, Mg, K, Ca) and trace (Sr, Ba, Mn, Li) elements, anions (HCO3−, NO3−, SO42−, Cl−), and Sr isotopic signatures. The current study identified the Sr isotopic signature in groundwaters from the Southern Carpathians and Apuseni Mountains karst areas of Romania and its relation to the water’s chemistry. The Sr concentration ranged between 16.5 and 658 µg/L, but in most groundwaters, it was below 200 µg/L. A considerable spatial variation and a low temporal variation, with a slightly lower Sr concentration in the winter than in spring, were observed. The strong positive correlation of the Sr with Ca, Mg, K, and Na indicated the common source of these elements. The main source of the Sr in groundwaters was the dissolution of carbonates, especially calcite, and dolomite to a lesser extent. The 87Sr/86Sr isotopic ratio ranged between 0.7038 and 0.7158. Generally, waters with a high Sr concentration and moderate 87Sr/86Sr ratios indicated carbonate dissolution, whereas samples with low Sr concentrations and high 87Sr/86Sr ratios suggested the dissolution of silicates.