Coastal wells are a commonly used intake method for seawater-source heat pump systems because they help mitigate biofouling and increase seawater temperatures. Coastal well water intake systems operate underground across both saturated and unsaturated zones. Therefore, a three-dimensional gas-liquid porous media seepage model of coastal wells was established based on COMSOL Multiphysics to conduct in-depth research on the seepage mechanisms and water intake behavior of coastal wells. The effects of parameters, such as well depth, pressure difference, well arrangement, and well spacing, on the seepage water intake system were studied. The results indicate that as the well spacing increases, the well depth and well flow rate increase, but the flow rate per unit well depth decreases. The flow rate of the coastal wells is directly proportional to the square difference between the coastline and coastal well porosity pressure. When the seawater hydrostatic porosity pressure difference between the coastline and coastal well was 5 m, the influence radius of the well seepage velocity was approximately 25 m. The velocity field was not affected when the distance between the two wells was greater than 50 m, regardless of whether the wells were arranged parallel or perpendicular to the coastline.