We develop a heat-transport model to study the impact of streambed morphology on temperature distribution within the hyporheic zone of gravel bed rivers. The heat transport model, which includes conduction, diffusion, and advection, is solved by a Lagrangian approach, neglecting transverse dispersion and considering stream water temperature as boundary condition at the streambed. First, we show that the model accurately reproduces the temperature distribution measured within the hyporheic zone of a reach of the Bear Valley Creek, Idaho (USA). Our model reveals spatially complex patterns of hyporheic water temperatures that vary with time within the hyporheic zone and at the streambed surface. The analysis shows that temperature distributions are primarily related to the hyporheic residence time and consequently to the bed morphology and in-stream flow discharge. Results show that the hyporheic temperature amplitudes are smaller than the surface water temperature and they decrease with stream size, leading hyporheic zones of large streams to be independent from in-stream daily temperature fluctuations.