The karst research community has known that traditional numerical groundwater flow codes ignore the non-Darcian, dual-permeability components of flow that can occur in karst aquifers. In this study, the potential limitations of using such tools are quantified by evaluating the relative performances of 3 groundwater flow models at a test-site near Weeki Wachee, Florida, in the dual-permeability Upper Floridan aquifer. MODFLOW-2005 and MODFLOW-2005 Conduit Flow Process (CFP), a Darcian/non-Darcian, dual-permeability groundwater flow code recently developed by the U.S. Geological Survey, are used in this study. A monitoring program consisting of discharge measurements and high frequency data from 2 springs and monitoring wells penetrating the matrix and conduit networks of a karst aquifer was initiated to characterize the test-site and constrain new parameters introduced with MODFLOW-2005 CFP. The monitoring program spanned conditions prior to, during, and following convective and tropical storm activity, and a drought. Analytical estimates for Reynolds numbers, ranging from 105 to 106, suggest that turbulent flow occurs in portions of the underlying conduit network. The direction and magnitude of fluid exchange observed between the matrix and conduit network indicate the conduit network underlying the test-site drains the matrix. Head differences and observed responses in monitoring wells penetrating the matrix and conduit network indicate that the hydraulic conductivities between the 2 networks do not significantly differ from each other. A conceptual model for the spatial distribution of preferential flow pathways using multiple data types, including shallow recession limbs observed in discharge hydrographs indicate a slow responding aquifer with a high storage capacity, and a poorly integrated conduit drainage network with little to no point recharge. Model performances were evaluated by comparing observed hydrographs for discharge and monitoring wells penetrating the matrix and conduit network following convective and tropical storm events, and drought conditions, to simulated values from transient simulations. Model statistics for 32 target wells and sensitivity analysis were included in the evaluation. The dual-permeability model using the MODFLOW-2005 CFP Mode 1 displayed the highest performance with improved matches ranging from 12 to 40% between simulated and observed discharges relative to the laminar and laminar/turbulent equivalent-continuum models.