I'm not sure if it counts, but the Core and Waterway segment from Cave Story, especially if you want to wait to get the good jetpack. The water level constantly changes when fighting the core and if you get stuck at the bottom right of the room when the water rises, you were royally fucked due to not being able to get some oxygen. The Waterway part can be really annoying with the currents being hard to swim into in some areas and then the tough jump you'll have to make if you want to save a major character since involves going from a low spot underwater, where movement is gimped to a somewhat far higher spot above water. It just felt like a chore.