Hmm, the first question, in my mind, is what game system are you using? That may make a difference, as each has their own rules.
Presuming D&D 3.5, I'd rule 4 feet of water to be more than simply "Difficult terrain".
Presuming firm footing is available (per the table in the DMG), characters can try walking at half speed. In water that deep swimming is a clear option. for Small and smaller creatures swimming may be the only option.
Creatures with a swim speed can obviously choose to use it. Effects like a Fly spell fall into the "none of the above" category on that aquatic combat chart. Move at normal speed, but be considered "off balance", and fight at normal aquatic penalties if under water.
Striking from air to water or water to air might be a question. My own thought is that if a strike begins or ends in any real depth of water, say a foot or more, then the underwater combat rules apply.
Depending on the water, it may offer true visual concealment. Most lakes and beaches I've visited, and a lot of rivers as well, are green water, not clear. Unless the water is in a very fresh water stream, it's a far cry from a nice chlorinated pool.
Per game rules visibility can vary from five to 100 feet. Shallow water is the most likely to be clouded, in my experience, either by turbulence or algae. Go into deeper water, away from the shore, an you get less sand and mud mixed in, and less in the water for the algae to feed on. So the four foot depth of the example suggests that we should think of Obscuring Mist and the like when it comes to perception in the water, particularly when looking from air to water or water to air.
Now add the agitation of a combat to the mix. People struggling for footing are going to stir up mud and sand, blood will act like smoke when something is wounded. There's a reason why most fish depend on sound far more than sight. In an aquatic environment, the creature limited to eyesight is at a severe disadvantage.
For combat: Medium creatures should be able to swing weapons normally at foes above the water. The hindrance of the water on movement, which would affect AC, would be balance by the effective cover the water gives. Someone with Freedom of Movement would be another matter.
The area from area effect spells generally doesn't cross the air/water barrier, so treat all targets as if they have partial concealment/cover.
If an air-breather goes unconscious and drops below water level they begin to drown immediately. Normally they'd have a grace period based on their CON score, but that's specifically or characters holding their breath. Unconscious creatures don't hold their breath. They make a CON check, DC 10 the first round, then again on each successive round with a cumulative one point penalty. The first time they fail they've inhaled water and are drowning/suffocating (see the Suffocation rules). Their real hit points drop to zero, and they're dying.