Modeling flow and transport using both temperature and dye tracing provides constraints that can improve understanding of karst networks. A laminar flow and transport model using the finite element subsurface flow model simulated the conduit connection between a sinking stream and spring in central Pennsylvania to evaluate how conduit morphology might affect dye transport. Single and overly tortuous conduit models resulted in high concentrations as dye flowed back into the conduit from the matrix after dye injections ceased. A forked conduit model diverted flow from the main conduit, reducing falling limb dye concentration. Latin hypercube sampling was performed to evaluate the sensitivity of 52 parameter combinations (conduit hydraulic conductivity, conduit cross-sectional area, matrix transmissivity, matrix porosity, and dispersivity) for four conduit geometry scenarios. Sensitivity of arrival time for 50% of the dye indicated no parameter combinations which simulate falling limb dye concentrations for tortuous geometries, confirming the importance of the forked geometry regardless of other parameters. Temperature data from high-resolution loggers were then incorporated into the forked conduit model to reproduce seasonal spring temperature using variable sink inflow. Unlike the dye trace models, the thermal models were sensitive to other model parameters, such as conduit cross-sectional area and matrix transmissivity. These results showed this dual approach (dye and temperature) to karst network modeling is useful for (1) exploring the role of conduit and matrix interaction for contaminant storage, (2) constraining karst conduit geometries, which are often poorly understood, and (3) quantifying the effect of seasonal trends on karst aquifers.