The changes in soil/rock structure caused by engineering disturbance or earthquakes could affect water chemistry by increasing the reaction surface, enhancing the oxidation condition, or exposing soluble rocks. However, the details of the mechanisms of the disturbance of soil/rock are little known. Based on the soil column experiment, this study analyzed the concentrations of sulfate (SO4), sulfur, and oxygen isotopic composition of SO4 (δ34S-SO4 and δ18O-SO4) in effluent water. The water–rock interaction mechanisms in the disturbed soil and the contribution of this interaction to the SO4 in groundwater were studied. The results suggest that the concentration of SO4 in the first effluent water sample can reach up to 97 mg/L, much higher than that in natural groundwater (6.8 mg/L). The isotopic composition of SO4 further suggested that SO4 in the first effluent water sample was mainly derived from the dissolution of SO4-containing evaporites. The proportion was estimated to be 93%. SO4-containing evaporites accounted for 23% of the SO4 content in all effluent water samples during the experiment. The disturbance of soil structure led to the exposure and dissolution of SO4-containing evaporites, which were initially insoluble under natural conditions. This study is essential to the clarification of the water–rock interaction mechanisms following the changes in soil/rock structures.