I'm not sure what the right approach here is. My game is a "realistic" side scroller, in that while there are magical elements, the characters are realistically proportioned humans who move realistically. Think gameplay vaguely like Abe's Oddesee. The storyline seems to have forced me to have an entire section of the game take place under water. I suspected it might, but in my original vision water played only a small role... now faced with creating an entire section based on it, I find myself at a loss. (It looks like water will make up perhaps 1/6th of the game.) The issue is that the gameplay focuses on platforming primarily: running, jumping, hoisting, crawling, that sort of thing. Water changes all that drastically. What I want to avoid is having a swath of my game be totally different from the rest. One option is to treat the water as a back drop, and just ignore it... that doesn't seem right to me, in a "realistic" world -- even if the character could breath and see fine via magic, she'd still need to "swim" instead of walking. Another option is to set up the level differently, let her swim, and suck up the fact that the controls are different. Does anyone have an example of a game that does this and made it work? In either case, the combat becomes problematic because it's based on water and fire spells. In the normal course of the game, the character can, for example, throw a fire dart. What will she do under water? It seems like fire magic would be out of the question, and how much effect could water have on creatures who live in water? I guess that's not a gameplay issue so much as a story justification issue. Any idea there would be helpful also! I'm just looking for some ideas on how to integrate the walking/running seamlessly with the swimming.

Ice magic seems like it would be very effective on underwater creatures as well as physically working within water.

I'm honestly having a hard time thinking of a platformer that doesn't have swimming. The Marios have water levels, the Sonics have water levels. There are a lot of platformers that have swimming in lava too, treating it as 'fire water' or something like that. I don't see a problem as long as you avoid having water be fatal in non-water levels; inconsistently fatal water is crappy.

What about electric attacks??
Maybe you could adjust the jump and walk speeds and distances to emulate near zero gravity. If not you could just use a mario or donkey kong country like swimming because like sunandshadow said, there are a lot of great platformers that use swimming.

If you want to keep the same controls, you could do it similar to Super Metroid: underwater the character still ran around and jumped, but it was slowed down, jumps went higher, and things fell slower.

If you don't want to create new attacks or get very "unrealistic" or inconsistent, you could make water attacks do no damage but push enemies around (or just treat it as blunt physical damage if you already have that as well), and fire attacks could cause steam bubbles which would work generally the same as usual but float upwards somewhat.

Fire could work just fine underwater. It would just be obscured by a trail of steam, and probably wouldn't go as far.

As for the controls, just make sure the player knows the exact moment that they switch, and go with it.

In the platformer game I've been working on water (and other liquids) have higher resistance (and thus lower terminal velocity), a lower effective gravity, and higher control on movement when off of the ground. It tends to work pretty well and blends into the rest of the game without a problem.

Thanks for all your input, guys. I'm going to prototype a couple solutions, and get back when I have something to show.

Like platinum said, lower the resistance.

Reduce every value that has anything to do with speed by a factor of X (I'd choose 2).
To save great workarounds you can let the main character jump underwater whenever it's falling (y speed > 0), making it look like it's swimming. Talking about physics here, not about graphics. You might have to develop a seperate spriteset for that.

Should save you a lot of time rebuilding things in the engine.

If she uses magic, why not have her inhabit an air bubble underwater? Wouldn't that fix a few issues? Perhaps it is stretching from the actual use of magic you intended however.

Since it overs 1/6th of your game, it may be worth actually making genuine mechanics associated with water. Think of the latest mario on wii. There isn't water everywhere, but they actually bothered making a swim animation (and trust me, nintendo never loses a penny developping something that is not worth it, if you don't believe me, check on the inteview about why there are two Tods and no Peach! It is priceless).