There are in fact 2 Dungeons after Rayquasa that have an water theme, Stormy Sea and Silver Trench. Both present powerful Water and Rock type enemies.
Stormy Sea is fairly difficult, sporting 40 floors and 20-35 Lv Pokemons and a powerful final boss.
Silver Trench on the other hand is undoubtedly one of the biggest challenges in the entire game, containing Lv 18-45 opponents spread across 99 floors and one of the most destructive bosses in the entire game.
If you want to venture into these dungeons, bring powerful Electric, Grass and Fighting types to deal with the monsters of the depths.