The only items worth obtaining underwater are the hidden Arceus Plates. Here they are:
(Note: when in the correct spot, circle around in that are and tap A like crazy. It helps you find the plate in that spot.)
Enter the underwater trench on the south side. If you investigate the area to the north, you can find a hidden Flame Plate. Just keep clicking the A button near the northern area.
Swim to the dead end in the east. If you search this area, you can find the Sky Plate hidden here.
Follow the trench as far north as you can, then swim it to a small dead end in the west. You may find three Luvdisc swimming around here. Search this area to find a hidden Mind Plate.
The underwater trench along the middle of the route has four points. Three legendary items can be found at three of them. Search the point all the way to the northwest to find a hidden Dread Plate. Just keep tapping the A button around the top of the point until you find it.
Search the third point towards the middle of the route to find a hidden Spooky Plate.
Search the fourth point to the east to find a hidden Insect Plate.
On the west side of the route is a circular sandbar. Use a Pokemon with Dive to go beneath the surface right in the middle of this sand bar. Dive into the trench on the outside of the circular sandbar. Near the northwest corner of the circular trench is a hidden Stone Plate.
Near the west side of the circular trench is a hidden Draco Plate. It's a short distance south of the Stone Plate.
Near the southeast side of the circular trench is a hidden Pixie Plate. It's in between the X-shape that the light from above makes, on the right side.
Swim to the southwest until you find a Pokemon trainer. Before battling him, search the bare spots in the seaweed to find a hidden Splash Plate.
Swim to the northwest and search another bare spot in a patch of seaweed to find a hidden Zap Plate.
Another bare spot in a patch of seaweed can be found to the south. This is just before Route 130. Search this area to find a hidden Toxic Plate.
If you dove into the trench from the west side, swim a short distance southeast to a bare spot in a patch of seaweed. You should find a hidden Icicle Plate here.
To the north is a Pokemon trainer. Before reaching him, investigate the large bare area south of the trainer. Around the middle of this area is a hidden Earth Plate.
After the battle, search the bare spot to the right of the trainer to find a hidden Meadow Plate.
Search the area just south of Scuba Diver Silas to find a hidden Fist Plate.
After beating the Pokemon League, return to Mossdeep City and head to Steven's house. Pick up the lone Beldum on the table, then take off the Iron Plate its holding to find the last plate.