In this study, a groundwater flow cycling in a karst springshed and an interaction between two springs, Spring Creek Springs and Wakulla Springs, through a subground conduit network are numerically simulated using CFPv2, the latest research version of MODFLOW-CFP (Conduit Flow Process). The Spring Creek Springs and Wakulla Springs, located in a marine estuary and 11 miles inland, respectively, are two major groundwater discharge spots in the Woodville Karst Plain (WKP), North Florida, USA. A three-phase conceptual model of groundwater flow cycling between the two springs and surface water recharge from a major surface creek (Lost Creek) was proposed in various rainfall conditions. A high permeable subground karst conduit network connecting the two springs was found by tracer tests and cave diving. Flow rate of discharge, salinity, sea level and tide height at Spring Creek Springs could significantly affect groundwater discharge and water stage at Wakulla Springs simultaneously. Based on the conceptual model, a numerical hybrid discrete-continuum groundwater flow model is developed using CFPv2 and calibrated by field measurements. Non-laminar flows in conduits and flow exchange between conduits and porous medium are implemented in the hybrid coupling numerical model. Time-variable salinity and equivalent freshwater head boundary conditions at the submarine spring as well as changing recharges have significant impacts on seawater/freshwater interaction and springs' discharges. The developed numerical model is used to simulate the dynamic hydrological process and quantitatively represent the three-phase conceptual model from June 2007 to June 2010. Simulated results of two springs' discharges match reasonably well to measurements with correlation coefficients 0.891 and 0.866 at Spring Creeks Springs and Wakulla Springs, respectively. The impacts of sea level rise on regional groundwater flow field and relationship between the inland springs and submarine springs are evaluated as well in this study.