Heat transport associated with current–bed form fluid exchange affects biogeochemical and ecological process in a variety of aquatic settings. We simulate turbulent flow over dunes, induced Darcy flow in sediments, and sediment heat transport forced by a diel variation of water column temperature. Heat conduction dominates when the water column current cannot induce rapid fluid exchange. Heat advection becomes important with increasing sediment permeability and/or current velocity, resulting in a complicated space-time temperature pattern. Weak temperature variations are found beneath dune crests, where water upwells out of the sediments; strong variations are located below dune stoss faces, where water downwells. The relative dominance of heat conduction versus advection is captured by a global Peclet number that depends on dune geometry, and hydrodynamic and thermal properties, including the period of thermal forcing. Thermally induced fluid viscosity variations cause periodic but nonsymmetric changes in fluid flux through the sediments, but do not significantly influence temperature patterns.