When you are engaged in naval combats, some Wall spells directly cast before the enemy ship are surprisingly effective. For example, a Wall of Fire should get rid of those nasty sails (and posiibly some sailors). Or imagine a galley in full speed, crashing against a Wall of Force .
Summoned Water Elementals (the bigger, the better) can also provide help with their vortex or stop/overturn vessel abilities. As we are already talking about summoned creatures: most "water-based" creatures in the summon list are much more powerful than "land-based" creatures of equal spell level. Try to escape from a grappling (giant) octopus!
When fighting underwater, remember to check with your DM if he allows spells with verbal components (some don't). Freedom of Movement comes in handy, or, even better, a Pearl of the Sirens (a magic item, though).