We investigate the effects of current–bed form induced flow and heat transport through permeable-bottom sediments overlain by a marine or terrestrial water column that is gaining or losing deep groundwater. Heat transport is forced by the diel variation of temperature in the water column. The investigation utilizes sequentially coupled simulations of turbulent flow in the water column, and Darcy flow and heat transport in the sediments. The simulations address the question when, where, and by how much are diel water column temperature variations transmitted into sediments subjected to ambient-groundwater discharge? This is crucial information for detecting, observing, and predicting temperature-sensitive biogeochemical and ecological processes in the bottom sediments. When the groundwater gain or loss is small, it has no appreciable effect on temperatures in the sediments, which are controlled by heat conduction and current–bed form induced heat advection. As losing discharge increases, the temperature signal from the water column penetrates deeper into the sediments, with the largest temperature variations found under a downwelling zone along the stoss side of the bed form and damped temperature variations found near a narrow upwelling zone below the crest. Similar patterns are observed under gaining conditions, but with temperature variations penetrating to shallower depths; the interfacial exchange zone is diminished by upward movement of deep groundwater. Large gains or losses of deep groundwater prevent the formation of an interfacial exchange zone making heat transport almost vertically one-dimensional. The sensitivity of the sediment-thermal regime to hydrodynamic conditions increases with increasing water column current (Reynolds number) and with sediment permeability.