WATER DANGERS

Any character can wade in relatively calm water that isn't over his head, no check required. Similarly, swimming in calm water only requires skill checks with a DC of 10. Trained swimmers can just take 10. (Remember, however, that armor or heavy gear makes any attempt at swimming much more difficult. See the Swim skill description.)
By contrast, fast-moving water is much more dangerous. On a successful DC 15 Swim check or a DC 15 Strength check, it deals 1d3 points of nonlethal damage per round (1d6 points of lethal damage if flowing over rocks and cascades). On a failed check, the character must make another check that round to avoid going under.
Very deep water is not only generally pitch black, posing a navigational hazard, but worse, it deals water pressure damage of 1d6 points per minute for every 100 feet the character is below the surface. A successful Fortitude save (DC 15, +1 for each previous check) means the diver takes no damage in that minute. Very cold water deals 1d6 points of nonlethal damage from hypothermia per minute of exposure.

Drowning

Any character can hold her breath for a number of rounds equal to twice her Constitution score. After this period of time, the character must make a DC 10 Constitution check every round in order to continue holding her breath. Each round, the DC increases by 1.
When the character finally fails her Constitution check, she begins to drown. In the first round, she falls unconscious (0 hp). In the following round, she drops to -1 hit points and is dying. In the third round, she drowns.
It is possible to drown in substances other than water, such as sand, quicksand, fine dust, and silos full of grain.