Exploring hydraulic connections between brine mining wells is of great significance to the development of geological resources; however, there are still challenges to accurately identifying these connections. In this study, a combination of hydrochemical and biological analyses was used to investigate the hydraulic connections between three saltworks (Yangkou, Hanting, and Changyi) in southern Laizhou Bay, China. The results showed that the groundwater recharge sources at Yangkou saltworks, and therefore the associated salts and hydrochemical composition of the brine, were different from those of the other two saltworks. The diversity and composition of the microbial community among the three saltworks were identified based on a high-throughput DNA sequencing method. The brines of Hanting and Changyi saltworks had greater similarity in terms of microbial diversity and composition, which was consistent with the hydrochemical results. Based on microbial analysis combined with hydrochemistry, the depths of the mining wells at Hanting saltworks were identified, along with the hydraulic connection with Changyi saltworks. As a tool to judge the hydraulic connections of geological reservoirs, microbial analysis combined with hydrochemistry may be applicable to a wider range of subsurface resources, such as oil and gas, which will provide new ideas for the rational development of underground resources.