The logging of submerged trees in Brazil was done by divers until too many of them were getting killed, plus boats were getting sank. The divers would go down with hydraulic saws and cut the trees off, and the trees would rocket to the surface, and smash the boat to smithereens. Now they use a hydraulic arm with a mechanical hydraulic cut-off saw like a feller-buncher has. The arm is mounted on a large trawler and there's an additional attachment that holds the tree in place while it is being cut.
In Brazil this logging has proven to be quite lucrative, since the hardwoods are preserved quite well even after having been submerged for 20+ years. Sort of like the guys in California who dive down and retrieve submerged Redwood and Sequoia logs.