When Pride is pinned down in the water one of the agents states 'Automatic weapon fire over there'. While the weapon was firing on automatic earlier, that took place before the agents had arrived. After they arrived there were only single shots.
Bullets lose almost all of their velocity when hitting water due to it being a non-compressable fluid. When Pride is being shot at while he is underwater, bullet trails are shown whizzing by him while he is many feet under water. The bullets would have broken up and pretty much stopped moving just after entering the water.