A method for burying a pipeline in a bed of a body of water which includes: making a trench with a bottom surface in a bed of a body of water via a bed working vehicle advanced in an advancing direction; advancing a floating unit in the body of water; releasing a pipeline in the body of water via a tensioner and along a lay device tilted in an adjustable manner and constrained to the floating unit; guiding the pipeline to the bottom surface of the trench via a guide vehicle advanced on the bed of the body of water; and controlling the tensioner, the floating unit, the lay device, the bed working vehicle, and the guide vehicle to minimize stress along the pipeline.