The Upper Permian Dalan Formation and the Lower Triassic Kangan Formation in the Persian Gulf area are mainly composed of shallow marine facies limestone and dolomite. Two subsurface-cored intervals were investigated in order to understand the original mineralogy and paleoceanic conditions. The decreasing trend of Sr concentration in these deposits shows that aragonite was precipitated during the Late Permian and then gradually changed to calcite toward the Permian–Triassic boundary (PTB). The dissolution rate of aragonite decreased from 60 m below the PTB toward the boundary, with the only exception at 10 m below the Permian-Triassic Boundary (PTB) due to the Permian–Triassic unconformity in this region. The increasing trend of Mg/Ca ratio in a global scale at the end-Permian time shows that the interpreted variation of mineralogy does not result from the change of this ratio. The increasing pCO2 and decreasing pH are considered to be the main controlling factors. The increase of Ca2+ at the end-Permian time due to the input of meteoric waters is too little to fully compensate this effect. A local maximum of the Si content just at the PTB confirms the input of runoff waters.