From my experience, not always the best worlds/levels.
- Water Temple from TLoZ: Ocarina of Time (the unfamous famous level)
- Dire Dire Docks from SM64
- Gloomy Galleon from DK64
- Great Bay Temple from Majora's Mask
Just to name a few. I'm sure these are only the tip of the iceberg and that worse water levels exist. Though, these are the ones that came to mind. Most of the time, it's not necessarily the level that is a nightmare, but the controls swimming or whatsoever.