Estuarine areas have emerged as promising sites for harnessing the hydrokinetic energy resource through Hydrokinetic Energy Converters (HECs); however, the effects of substantial fluvial inputs on the energy resource and the performance of HECs have not been adequately investigated. With this in view, in this piece of research the seasonal variability of the site‐specific performance of a Savonius third‐generation HEC operating in the Miño Estuary (NW Spain) is investigated by considering several seasonal discharge scenarios. A shallow water hydrodynamic numerical model is implemented in its 2DH form and validated against water level and velocity observations. The results obtained highlight the need for accurate hydrodynamic modelling when planning the exploitation of the hydrokinetic resource in shallow estuaries subject to the combined influence of river and tidal flow, where the site‐specific performance of HECs could be significantly affected. Finally, the approach presented may be used in other areas suitable for hydrokinetic energy exploitation.