When in doubt, use the SRD:
http://www.d20srd.org/filters/monster.php
It yielded the following list when filtered for Aquatic:
Monster Size/Type Environment CR Alignment
Allip Medium Undead (Incorporeal) Any 3 Neutral Evil
Animated Object, Colossal Colossal Construct Any 10 Neutral
Animated Object, Gargantuan Gargantuan Construct Any 7 Neutral
Animated Object, Huge Huge Construct Any 5 Neutral
Animated Object, Large Large Construct Any 3 Neutral
Animated Object, Medium Medium Construct Any 2 Neutral
Animated Object, Small Small Construct Any 1 Neutral
Animated Object, Tiny Tiny Construct Any 1/2 Neutral
Baleen Whale Gargantuan Animal Warm Aquatic 6 Neutral
Cachalot Whale Gargantuan Animal Temperate Aquatic 7 Neutral
Devourer Large Undead (Extraplanar) Any 11 Neutral Evil
Dinosaur, Elasmosaurus Huge Animal Warm Aquatic 7 Neutral
Dire Rat Small Animal Any 1/2 Neutral
Dire Shark Huge Animal (Aquatic) Cold Aquatic 9 Neutral
Doppelganger Medium Monstrous Humanoid (Shapechanger) Any 3 Neutral
Dragon Turtle Huge Dragon (Aquatic) Temperate Aquatic 9 Neutral
Elf, Aquatic Medium Humanoid (Elf) Temperate Aquatic 1/2 Chaotic Good
Gargoyle Medium Monstrous Humanoid (Earth) Any 4 Chaotic Evil
Gargoyle, Kapoacinth Medium Monstrous Humanoid (Aquatic) Any Aquatic 4 Chaotic Evil
Ghoul Medium Undead Any 1 Chaotic Evil
Ghoul, Ghast Medium Undead Any 3 Chaotic Evil
Ghoul, Lacedon Medium Undead (Aquatic) Any Aquatic 1 Chaotic Evil
Golem, Clay Large Construct Any 10 Neutral
Golem, Flesh Large Construct Any 7 Neutral
Golem, Greater Stone Huge Construct Any 16 Neutral
Golem, Iron Large Construct Any 13 Neutral
Golem, Stone Large Construct Any 11 Neutral
Hag, Sea Medium Monstrous Humanoid (Aquatic) Temperate Aquatic 4 Chaotic Evil
Homunculus Tiny Construct Any 1 Any
Kraken Gargantuan Magical Beast (Aquatic) Temperate Aquatic 12 Neutral Evil
Locathah Medium Humanoid (Aquatic) Warm Aquatic 1/2 Neutral
Lycanthrope, Wererat Medium Humanoid (Human, Shapechanger) Any 2 Lawful Evil
Manta Ray Large Animal (Aquatic) Warm Aquatic 1 Neutral
Merfolk Medium Humanoid (Aquatic) Temperate Aquatic 1/2 Neutral
Mohrg Medium Undead Any 8 Chaotic Evil
Mummy Medium Undead Any 5 Lawful Evil
Mummy Lord Medium Undead Any 15 Lawful Evil
Naga, Water Large Aberration (Aquatic) Temperate Aquatic 7 Neutral
Octopus Small Animal (Aquatic) Warm Aquatic 1 Neutral
Octopus, Giant Large Animal (Aquatic) Warm Aquatic 8 Neutral
Ogre, Merrow Large Giant (Aquatic) Temperate Aquatic 3 Chaotic Evil
Orca Huge Animal Cold Aquatic 5 Neutral
Porpoise Medium Animal Temperate Aquatic 1/2 Neutral
Rat Tiny Animal Any Any 1/8 Neutral
Sahuagin Medium Monstrous Humanoid (Aquatic) Warm Aquatic 2 Lawful Evil
Sea Cat Large Magical Beast Temperate Aquatic 4 Neutral
Shadow Medium Undead (Incorporeal) Any 3 Chaotic Evil
Shadow, Greater Medium Undead (Incorporeal) Any 8 Chaotic Evil
Shark, Huge Huge Animal Cold Aquatic 4 Neutral
Shark, Large Large Animal Cold Aquatic 2 Neutral
Shark, Medium Medium Animal Cold Aquatic 1 Neutral
Shield Guardian Large Construct Any 8 Neutral
Spectre Medium Undead (Incorporeal) Any 7 Lawful Evil
Sprite, Nixie Small Fey (Aquatic) Temperate Aquatic 1 Neutral
Squid Medium Animal (Aquatic) Temperate Aquatic 1 Neutral
Squid, Giant Huge Animal (Aquatic) Temperate Aquatic 9 Neutral
Swarm, Rat Tiny Animal (Swarm) Any 2 Neutral
Tarrasque Colossal Magical Beast Any 20 Neutral
Triton Medium Outsider (Native, Water) Temperate Aquatic 2 Neutral Good
Troll, Scrag Large Giant Cold Aquatic 5 Chaotic Evil
Vampire Spawn Medium Undead Any 4 Any Evil
Wight Medium Undead Any 3 Lawful Evil
Wraith Medium Undead (Incorporeal) Any 5 Lawful Evil
Wraith, Dread Large Undead (Incorporeal) Any 11 Lawful Evil
Zombie, Human Commoner Medium Undead Any 1/2 Neutral Evil