In order to use near-field measurements to obtain signature of a signal penetrating seafloor in a shallow water surveyed area, the water-bottom reflections' effect is removed. The removal is performed by obtaining first a far-field initial estimate from stacked primary pulses in the near-field measurements, and then estimating water-bottom reflection portions for different depths using differences between the near-field measurements and the far-field initial estimate. The signature of the air-gun for each shot is then deblended from the near-field measurement for the shot using the one of the water-bottom reflection portions according to a water-bottom depth associated with the shot location.