To submerse is to go below the surface of water. When you watch a seabird submerse, you see it dive completely under water, probably so that it can catch a fish.
You can use the verb submerse in much the same way you'd use submerge, to mean "sink or dive under the surface of the water." The meaning of submerse makes sense when you know that a submersible is a small underwater vessel, similar to a submarine. All of these words have the Latin prefix sub- in common, which means "under." Merse comes from the Latin verb "to plunge," mergere .