The following are some key rules to remember about fighting underwater.¹

Invisibility

An invisible creature displaces water and leaves a visible, body-shaped “bubble” where the water was displaced. The creature still has concealment (20% miss chance), but not total concealment (50% miss chance).

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.

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.

Kerensky’s freezing sphere

When using the spell Kerensky’s freezing sphere underwater, you have two options.

1. the globe of cold energy streaks through the water to the location within range you select, freezing water in a line from you to that point. Any creatures touched by the line are trapped, and take damage, as described; or,
2. the same effect, but in a 30-ft cube which originates at your position.

¹ This assumes that you've solved the movement/melee issue (with freedom of movement or a similar effect) and the breathing issue (with water breathing spells, necklaces of adaptation, etc.). If you haven't, then you need to somehow deal with those things too (and sucks to be you):

The penalties related to melee combat underwater without a freedom of movement spell are summarized in the table here: http://www.d20srd.org/srd/wilderness.htm#aquaticTerrain.

The mechanics of drowning are described here: http://www.d20srd.org/srd/environment.htm#waterDangers.

Recall that certain monsters and magical effects are able to override your normal ability to hold your breath, and require you to start making Constitution checks immediately.