We have measured the thermopower across the metamagnetic transition of the heavy fermion compound CeRu2Si2 at temperatures down to 0.1K and magnetic fields up to 11.5T. We find a large negative enhancement of the thermopower on crossing the metamagnetic field, as well as a sudden change in slope. We argue that this is consistent with the Zeeman-driven deformation of the Fermi surface through a topological transition. The field dependence of the thermopower highlights the discrepancy between thermodynamic and transport properties across the metamagnetic transition.