Whether transgression in the Bohai Bay Basin exist has been a matter of debate. The significance of this study is that it emphasises the application of paleosalinity indicators to interpret the paleoenvironmental changes correctly and to judge whether offshore lake basins are affected by seawater. In order to study the paleosalinity of the ancient water body and reconstruct the depositional environment when Shahejie formation deposited, the composition of clay minerals and elemental geochemical analysis were carried out. In this study, B/Ga and Sr/Ba ratios are sensitive to paleosalinity, indicating the ancient water body had mixed with fresh and salt-water. Paleosalinity calculated with Couch's method by boron content is 4.29‰-13.16‰ and with an average value of 7.79‰. These results indicated that the ancient water body of Qikou sag in Shahejie formation has typical brackish water characteristics or rather belongs to mesohaline water. In terms of the trend of the Sr/Ba and B/Ga ratios, as well as Sp, from Es3 to Es1s formation, the paleosalinity of the water body first increased and then decreased. The paleoclimatic analysis shows that the Qikou sag had warm and humid paleoclimate, and this climate was conducive to increasing the weathering intensity and the input of surface runoff. The changes of paleosalinity have no inevitable relationship with climate, and the brackish water environment during the Shahejie formation deposited is possibly related to transgression event, which allows salt water to invade and lead to the mixed water.