Computing device, computer instructions and method for processing energy at a free-surface reflection relating to an air-water interface. The method includes receiving input seismic data recorded with seismic sensors; receiving wave-height data that describes an actual shape of a top surface of a body of water; processing up-going energy at a receiver and down-going energy following a reflection at the sea-surface, using the input seismic data and a linear operator modified to take into account the wave-height data; and generating an image of the subsurface based on the up-going energy or the down-going energy or a combination of the input seismic data and one of the up-going or down-going energy.