Well, I'm not sure exactly which bubble is which item since I got them already, but I can spitball a few locations that could potentially be missed.
The alcove on the left side of the left well when getting the silver coins.
The little tunnel above the moving walls right after the first two spinning half-spiked wheels.
After the second set of spiked wheels when you get to land again, raise the water level once, then jump into the building right to the left of the second ship wheel that raises the water level again.
After raising the water level twice, jump onto the roof to the far left.
After draining the water from the chick's house, there's those two behind the windows to the right of the plug.
When the fisherman pulls you up, press up until you're in the back plane, then jump behind him and across the rooftops until you come across three bubbles. (That totally might be the one you're after.)