Historically, waterways were one of the most important modes of travel and communication within and between countries. On the other hand, characters on foot will find that lakes, rivers, and streams often block their travels in the wilderness. What's more, underground streams, cisterns, sewers, and moats are all part of the dungeon environment.
Water presents adventurers with five general problems. First, it's an obstacle that can block their movement. Second, characters in the water face the danger of drowning or losing gear. Third, a character caught in fast-moving water can be swept away from the rest of his party and battered or killed by rapids and waterfalls. Fourth, really deep water deals damage from the great pressure it exerts. Finally, exposure to cold water can be dangerous, afflicting characters with hypothermia.
The skills most commonly used in dealing with water as an obstacle are Swim and Profession (sailor). Unfortunately, not every character who gets into the water has these skills.
Any character can wade in relatively calm water that isn't over his head, with 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, page 84 of the Player's Handbook.)
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.