From the
SRD:
Underwater Combat
Land-based creatures can have considerable difficulty when fighting in water. Water affects a creature’s Armor Class, attack rolls, damage, and movement. In some cases a creature’s opponents may get a bonus on attacks. The effects are summarized in the accompanying table. They apply whenever a character is swimming, walking in chestdeep water, or walking along the bottom.
Ranged Attacks Underwater
Thrown weapons are ineffective underwater, even when launched from land. Attacks with other ranged weapons take a -2 penalty on attack rolls for every 5 feet of water they pass through, in addition to the normal penalties for range.
Attacks from Land
Characters swimming, floating, or treading water on the surface, or wading in water at least chest deep, have improved
cover (+8 bonus to AC, +4 bonus on Reflex saves) from opponents on land. Landbound opponents who have
freedom of movement effects ignore this cover when making melee attacks against targets in the water. A completely submerged creature has
total cover against opponents on land unless those opponents have freedom of movement effects. Magical effects are unaffected except for those that require attack rolls (which are treated like any other effects) and fire effects.
Fire
Nonmagical fire (including
alchemist’s fire) does not burn underwater. Spells or
spell-like effects with the fire descriptor are ineffective underwater unless the caster makes a
Spellcraft check (DC 20 + spell level). If the check succeeds, the spell creates a bubble of steam instead of its usual fiery effect, but otherwise the spell works as described. A supernatural fire effect is ineffective underwater unless its description states otherwise. The surface of a body of water blocks line of effect for any fire spell. If the caster has made a
Spellcraft check to make the fire spell usable underwater, the surface still blocks the spell’s line of effect.
(Table edited out -- check the link above)
