The phenomenon of salt water distributing in the upper aquifer and fresh water distributing in the lower aquifer exists for a long time in North China Plain. Nowadays, fresh water in the lower aquifer is threatening by the downward migration of salt water. Based on the water quality change around the borehole XK4 before and after the borehole GK with non-sealing walls being repaired, the mechanism of salinization caused by the borehole with non-sealing walls was investigated by building the solute transport model considering cross strata pollution. The results show that the transfluence occurs between the adjacent aquifers, which have faint hydraulic connection, through the borehole with non-sealing walls. Salt water in the upper aquifer migrates downward along the well tube and enters into the fresh water aquifer causing the salinization. The radius of the pollution halo of the borehole GK reaches 20~75 min 14 months, and the mineralization degree of water in the borehole XK4 increases by five times in five months. After the borehole GK was filled, the pollutant diffused and diluted, and the fresh water recovered to the original concentration in four months. The cross strata pollution caused by the borehole with non-sealing walls should attract enough attention and corresponding measurements should be taken.