We explore the mechanisms of heat transfer in a turbulent constant heat flux-driven Rayleigh–Bénard convection flow, which exhibits a hierarchy of flow structures from granules to supergranules. Our computational framework makes use of time-dependent flow networks. These are based on trajectories of Lagrangian tracer particles that are advected in the flow. We identify coherent sets in the Lagrangian frame of reference as those sets of trajectories that stay closely together for an extended time span under the action of the turbulent flow. Depending on the choice of the measure of coherence, sets with different characteristics are detected. First, the application of a recently proposed evolutionary spectral clustering scheme allows us to extract granular coherent features that are shown to contribute significantly less to the global heat transfer than their spatial complements. Moreover, splits and mergers of these (leaking) coherent sets leave spectral footprints. Second, trajectories which exhibit a small node degree in the corresponding network represent objectively highly coherent flow structures and can be related to supergranules as the other stage of the present flow hierarchy. We demonstrate that the supergranular flow structures play a key role in the vertical heat transport and that they exhibit a greater spatial extension than the granular structures obtained from spectral clustering.