Underwater or otherwise water-centric (sailing) campaigns for D&D Are generally set up from the start as a campaign focused around the water or underneath it. Races will be adapted for wet environments, every actually puts skill ranks in the Swim skill, and everyone makes dexterity-based characters because no one wants to be the person in heavy armor who sinks and then drowns before they can get out of their armor. At this point, handling underwater combat, the drowning rules, and how movement works is fairly academic. It is just one more bit of math that needs to happen for the players to take their turns and determine their actions.
You generally do not see a lot of mixing water environments and non-water environments. It happens occasionally, as most land-based campaigns need to cross water at some point. Oceans, rivers, lakes, marshes, and underground lakes in dungeons are all fairly popular. At that point, the players are forced to scramble. If they have time to prepare, a typical Dungeons and Dragons part can figure out a way to get everyone across safely and have a few plans in place for accidents. If they’re just shown a bit of water they have to cross in a dungeon, they will still plan. Their resources are just somewhat more limited.
Unless the campaign established that water environments are going to be a big part of the campaign, most of the players probably won’t look up the rules for swimming. The rules are fairly straight-forward. The swimming skill check to move around in water is dependent on the type of water. Still water is very easy, while flowing water is harder, floods are harder still, and stormy oceans or rocky rapids in rivers are incredibly dangerous. When swimming underwater, there are a few more things to consider, such as how long the character can hold their breath, what can affect that (fighting something underwater makes them run out of breath more quickly), and then what happens once they run out of breath. The rules are pretty brutal, but so is water. If the water is still enough that the checks are easy, some good common-sense practices like having a plan for extra air (extra-dimensional storage spaces are often full of air) or knowing how far you have to go to get back to the surface are a must.
Unfortunately, those do not always happen. After a few sessions involving water, including a couple close-calls, on of my players finally had a character drown. The character was a Halfling, so his movement was barely worth mentioning underwater, even though I’ve house-ruled half-speed movement instead of the usual quarter, and though he had plenty of rounds for holding his breath, he spent a lot of them fighting something because he tried to be invisible underwater as a means of sneaking past the security octopus. Invisibility is mostly ineffective in water, since an invisible person still displaces water, and there’s very little other cover to provide a means of effectively stealthing your way up to an octopus for a sneak attack.
The rest of the party, of course, helped him kill the octopus, but the Halfling couldn’t make it back to the surface in time, failed his constitution checks to survive, and then died before anyone could get him to the surface since no one else was a very strong swimmer. Tragic, of course. The scout then set a land-speed record for getting his body back to the druids for reincarnation because that isn’t his original body and a standard Raise Dead spell wouldn’t exactly work the way they wanted. But that’s a story for another day.
Sticking aquatic environment adventures into my dungeons is always a tricky concept. I had two possible traps that involved water in the first dungeon my players encountered, but the plan for those dungeons was to radically shift the campaign if the party got trapped by them, since it would have swept them all away. I left them out for a while, because the party wouldn’t really have an answer for them and they’re difficult to deal with. Also, to be entirely fair, the number of monsters and creatures that’d maintain water features in dungeons instead of just living in underwater dungeons is rather small. There just isn’t much of a need for them in most low-mid to mid level adventures. There’s plenty of other ways to kill a party. At the same time, water can be a great equalizer. Unless they’re specifically prepared for it, a high-level party has no advantage over water that a low-level party wouldn’t have as well. Drowning can kill anyone, no matter their level.
If you want some good resources on water combat, D20SRD.org has some useful information and the SRD section of dandwiki.com contains a lot of important info as well. Otherwise, feel free to make it up when you need it. Just make sure to write it down so you’re consistent. As I said when the Halfling drowned, “Everyone has to follow the rules, even the DM.” Once you set a rule, stick to it.