© 2019 Seawater intrusion due to sea level rise and climate change could significantly contaminate coastal groundwater resources, particularly in Florida, the flat low-land state in the United States. Based on the field investigation and hydrological measurements, a three-dimensional SEAWAT model is developed to evaluate the groundwater flow cycling and seawater intrusion to freshwater system in the Woodville Karst Plain (WKP), a typical karst groundwater system in the Floridan aquifer. The karst conduit network in the aquifer acts as fast flow pathway for groundwater flow and solute transport, so seawater could deeply intrude into the aquifer. Wakulla Spring, an inland spring 17 km from the coast and a coastal submarine spring, Spring Creek Spring Complex are connected through the conduit network. The flow direction between the two springs switches under various rainfall conditions in this region, thus the discharges at two karst springs are used to estimate the location of seawater/freshwater mixing interface. The SEAWAT modeling results indicate that the mixing interface, defined as 2 PSU (Practical Salinity Unit), intrudes 3 to 5 km through the subsurface karst conduit during the dry season and severely contaminates nearly 1 km width of groundwater around the conduit. The salinity distribution and the distance of seawater intrusion through the conduit system are very sensitive to precipitation variation and the sea level boundary condition. Furthermore, predictions are made for seawater intrusion to the aquifer under various sea level rise, precipitation scenarios and water pumping. The results show that the seawater intrusion could reach and contaminate inland freshwater systems if sea level rises 1.0 m or during a long-term no-precipitation season. This study provides insights for modeling and predicting the vulnerability of a coastal karst aquifer through the simulation of variable-density flow.