Previous studies, motivated by understanding water quality, have explored the mechanisms for heat transport and heat exchange in surface streams. In karst aquifers, temperature signals play an additional important role since they carry information about internal aquifer structures. Models for heat transport in karst conduits have previously been developed; however, these models make different, sometimes contradictory, assumptions. Additionally, previous models of heat transport in karst conduits have not been validated using field data from conduits with known geometries. Here we use analytical solutions of heat transfer to examine the relative importance of heat exchange mechanisms and the validity of the assumptions made by previous models. The relative importance of convection, conduction, and radiation is a function of time. Using a characteristic timescale, we show that models neglecting rock conduction produce spurious results in realistic cases. In contrast to the behavior of surface streams, where conduction is often negligible, conduction through the rock surrounding a conduit determines heat flux at timescales of weeks and longer. In open channel conduits, radiative heat flux can be significant. In contrast, convective heat exchange through the conduit air is often negligible. Using the rules derived from our analytical analysis, we develop a numerical model for heat transport in a karst conduit. Our model compares favorably to thermal responses observed in two different karst settings: a cave stream fed via autogenic recharge during a snowmelt event, and an allogenically recharged cave stream that experiences continuous temperature fluctuations on many timescales.