Here's how I handled it with my 4e party:
First, I decided that for flavor reasons I didn't want the party worrying about drowning, so I had Papuvin go into his cave and harvest a few precious leaves from a mysterious plant to give to the party. He wrapped his fiery hands in a wet towel in order not to burn the leaves. Each one of these Magus Leaves, when chewed and swallowed, would let a creature breathe underwater for 30 minutes.
Next, I allowed the PCs the use of rowboats if they wanted them (three to a boat). Three of the PCs decided to row while the others swam.
Finally, I ignored the movement rule under Athletics that says a non-aquatic creature moves at half speed underwater with a successful Athletics check. If the PC made the check, I let them move at full speed. I had also earlier given the party a custom pair of magic boots that let the wearer walk across water for a turn, and I ruled on the fly that they would also let the wearer walk at normal speed with no Athletics check on the bottom of a body of water.
The battle with Indomitability started in the water, with the Wizard trying to trap the beast in a Web, but eventually moved to shore. They probably did about 1/3 of the damage to Indomitability in the water and the rest on land.