Delfino Plaza only floods once. If you missed it, it's over. The water shouldn't kill you unless Mario suffocates under it while swimming. If you stay above, you'll be fine. It's actually quite fun to swim around for hours on end in the flooded Plaza, but you'll have to get on with the game eventually.

Alternatively, you have to use the Rocket Jet Pack (get used to it, because the Final battle also requires the Rocket Jetpack) to get to Corona Mountain without the flood. Simply walk in, and the level will start.

The last level is more of your basic timing and micromanagement. You'll have to steer the boat from Point A to Point B, a straight line that is riddled with stalagmites, which killed me more often than not. Water shouldn't be a problem, because you get free refill packs every 1/3 of the way. Break open the Rocket container, and hop up onto the clouds.

By the way, Corona Mountain is toward the giant-ass mountain behind the Shine Tower.