Yes, the gameplay in the water (in wholly filled or partially filled levels) can also be really fun or irritating depending on the ammo choice, and specifically how much of that ammo is in the level. For example, seekers are WAAAAY over-powered in most water levels (because it's hard to aim other weapons, as Stijn said. They are also over-powered especially if there is a water control room in the level.) So if you'd want that type of weapon in your level, make it VERY RARE if you're putting in any.
Anyways, I second Hitch.