A method for the cutting of underwater structures below the level of the sea bottom on which they are installed, comprises determining an ideal plane of cutting, having considered the characteristic features of the structure i.e. its morphology and its positioning on the bottom, the shape and consistency of the bottom itself, and the depth below the level of the bottom at which the cut must be effected; positioning and anchoring of a cutter in proximity of the cutting area; obtainment of at least one perforation or boring in proximity of the structure through the bottom at least up to the predetermined level for the cutting of the structure, along a direction parallel to the cutting direction and preferably lying on the cutting plane; and introduction of the cutter inside the perforation or boring and cutting of the structure. An apparatus for carrying out the method is also provided.