Seawater intrusion into onshore aquifers represents a significant environmental threat worldwide especially in this new era of climate change and sea water rise. This is the case at the Zhoushan Islands located in Hangzhou Bay (China). Precise monitoring of the position of the boundary between freshwater and saltwater is of utmost importance for water resource management especially in fractured bedrock. We use the Transient ElectroMagnetic (TEM) method to locate a salt plume in an area where two sets of faults-oriented NW-SE and NE-SW are connected to the sea in a rhyolitic substratum. The survey comprises 558 Transient ElectroMagnetic (TEM) soundings. The inverted resistivity data are combined with borehole logging data to underline the areas of groundwater salt concentration in the aquifer. This salinization is taking place along the pervasive fault zones indicating the role of these faults in channeling the salty water through the rhyolitic bedrock. This study underlines the critical role of faults pathways in the groundwater mineralization issues faced by coastal aquifers in fractured crystalline substratum.