Soil salinity plays an essential role in the growth of mangroves. Mangroves usually grow in intertidal zones. However, in Karimunjawa National Park (KNP), Indonesia, mangroves are also found in supratidal zones. Thus, this study aims to determine why mangroves can grow in this supratidal zone, even during the dry season. We analyze seasonal changes in groundwater flow and salinity dynamics using the hydraulic head, shallow groundwater salinity, and electrical resistivity imaging (ERI) data. The result shows that variation in groundwater salinity is caused by seawater intrusion, which is generated by a hydraulic gradient due to the sea level being higher than the water table in KNP. Rainfall and evapotranspiration, which change seasonally, likely affect the water table fluctuation and salt concentration. ERI images indicate this seawater intrusion in the top sediment up to the bedrock boundary. However, the resistivity difference in the wet and dry seasons shows that remarkable resistivity change occurs at the deeper layer (50–60 m below ground level (BGL)), likely due to freshwater recharge from rainwater on the land side. Groundwater in the KNP is shallow and saline; thus, mangroves in this zone, e.g., Ceriops tagal and Lumnitzera racemosa, can grow because their roots can reach this groundwater. These mangrove species can still grow in this zone even though the shallow groundwater is very saline (46–50 ppt). However, this condition might cause these mangroves to grow stunted. Thus, freshwater availability is crucial for mangrove growth in this supratidal zone to dilute this high groundwater salinity.