I've always enjoyed the water dungeons in the Zelda series. Be it OoT, MM or TP, those dungeons were always very non-linear with many options left for the player to go, and this is the very spirit of Zelda, the thing that has been making the series unique since it started: exploration. In all of these dungeons you have a central room from which you can choose multiple ways to go. Finding a key or opening a new passage in these dungeons always feels like a big achievement to me because you know you've done something right.
What adds to that is the 3D effect: In water, not only can you go left, right, back and front but you can also freely go up and down, this adds extra depth to the gameplay.
And I didn't find those levels very scary or creepy at all, IMO in OoT the Forest and Shadow temples were much creepier than the Water Temple and in TP the same holds true for the ice and desert dungeons (forgot their exact names). Honestly I hope that there will be a huge water dungeon in SS again, with even more paths to choose from (maybe 8 ways per floor) and even more 3D interaction between the floors, maybe they could combine the different water levels from the OoT Water Temple with the currents system from MM's Great Bay Temple to make a really big and challenging dungeon!
