Karst aquifers exhibit a dual flow system characterized by interacting conduit and matrix domains. This study evaluated the coupled continuum pipe-flow framework for modeling karst groundwater flow in the Madison aquifer of western South Dakota (USA). Coupled conduit and matrix flow was simulated within a regional finite-difference model over a 10-year transient period. An existing equivalent porous medium (EPM) model was modified to include major conduit networks whose locations were constrained by dye-tracing data and environmental tracer analysis. Model calibration data included measured hydraulic heads at observation wells and estimates of discharge at four karst springs. Relative to the EPM model, the match to observation well hydraulic heads was substantially improved with the addition of conduits. The inclusion of conduit flow allowed for a simpler hydraulic conductivity distribution in the matrix continuum. Two of the high-conductivity zones in the EPM model, which were required to indirectly simulate the effects of conduits, were eliminated from the new model. This work demonstrates the utility of the coupled continuum pipe-flow method and illustrates how karst aquifer model parameterization is dependent on the physical processes that are simulated.