Although it has gotten mixed reviews here at EN World, I'd recommend
The Deep by Mystic Eye Games, possibly coupled with
Boundless Blue by Goodman Games.
There are many aquatic references in the WotC books to consider, such as:
Savage Species
RACES: merrow, triton, scrag, water elemental
EQUIPMENT: pincer staff, sharktooth staff, aboleth mucus, Fishgutter scimitar, Staff of the Whip, Wave Piercer trident, liquid vortex,
TEMPLATES: half-merrow, anthropomorphic squid/octopus/shark
PRESTIGE CLASSES: Waverider, scaled horror
Fiend Folio
MONSTERS: aquatic oozes (bloodbloater, flotsam reekmurk), bog giant, demon (myrmyxicus, skulvyn, wastrilith), kelp angler, kelpie, sea drake, octopus tree, terlen, vine horror, yurian,
TEMPLATES: half-scrag
GRAFT/SYMBIONT: aboleth grafts
Monster Manual II
RACES: sirene, ixitxachitl, morkoth
MONSTERS: topaz dragon, elemental weird (water), ocean giant, kopru, legendary shark, leviathan, megalodon, ocean strider, teratomorph,
TEMPLATE: tauric (squid, octopus, etc)
Monster Manual
RACES: aquatic elf, kuo-toa, locathah, merfolks, merrow, sahuagin, skum, water elemental, water mephit, triton
MONSTERS: aboleth, chuul, dire shark, dragon turtle, giant octopus, kraken, octopus, sea cat, sea hag, shark, squid, water naga, bronze dragon, black dragon, tojanida
BoVD
VARIANT RULES: hivemind (school?)
EQUIPMENT: agony (liquid pain)
DEITIES: Yeathan, Demogorgon
Masters of the Wild
PRESTIGE CLASSES: Marinelord, King/Queen of the Sea
Defenders of the Faith
DEITIES: Bliodoolpoolp, Deep Sahelas, Eadro, Panzuriel, Sekolah, Demogorgon, Ben-Hadar, Olhydra
Arms and Equipment Guide
Aquatic Exotic Troops (merfolk, sahuagin, triton), Guard Creatures (sea lion), Mounts (hippocampus, Zaratan), Vehicles (gnome submersible, Nautilus), Arms & Armor (coral, shell, chitin)
Tome & Blood
PRESTIGE CLASSES: Elemental Savant
Song and Silence
PRESTIGE CLASSES: Dread Pirate
Manual of the Planes
Elemental Plane of Water, River Oceanus, River Styx, Abysm (Abyss), Porphatys (Carceri), Stygia/Sheyruusk (Nine Hells), Silver Sea (Seven Heavens), Thalasia (Elysium), Aquallor (Arborea)
MONSTERS: marid
TEMPLATE: half-elemental (water)