The reason it looked like it was coming from the bellhousing area while you were running it, is because the flywheel was churning up the water once it got about an inch or two deep.
Before dragging it out to a ramp to check it, just fill it a couple inches deep around the pump and then look underneath the boat to see where it leaks out. Some possibilities would be transom adapter gasket, o-ring between bowl and T/A, pump intake needing resealing....
If the water ever got deep enough to soak the thrust bearing of the pump, be sure hit it with a fresh load of grease.