The coastal Sanshandao mine is threatened by the overlying Quaternary water and seawater. Following an introduction to the geology and hydrogeological conditions in the mine area, a detailed hydrogeological survey and sampling were conducted and hydrochemical and stable isotopic (δ2H and δ18O) tests on various waters were carried out to characterize the origin of water in the mine tunnels. Investigation and statistical analysis indicated that the northwest-trending fractures with large dip angles and long trace lengths are well developed in the northeast compared with those in the southwest of the mine. The permeability coefficients of the rock masses are in the range 4.19 × 10−8–2.25 × 10−5 m/s, indicating that the fractured rock masses have generally low permeability. The seepage water had higher values of EC, total dissolved solids, and concentrations of most elements than the seawater and saline groundwater. Besides, the isotope composition of the waters indicated that the seepage water was more isotopically enriched than seawater but less than brine. The proportions of the three different sources were calculated based on hydrochemical and isotopic analyses. Overall, the mine water was composed of 72% seawater, 14.8% brine, and 13.2% atmospheric precipitation, respectively. Therefore, some preventive measures are essential to avoid the probability of seawater inrush.