I would say "No" but with conditions.
If you were throwing a Fireball into a Lake, I would say the lake would change how the fireball behaves. It wouldn't set things on fire but it would probably cause a huge volume of water to insta-boil or maybe even flash to steam. Or both. But I'd leave damage and the area of the effect unchanged. I'd say that weaker fire effects would just be snuffed out unless you think they're hot enough to actually burn underwater.
Hitting something with a Ranged Touch Attack or something underwater, you might rule that the target underwater has some measure of concealment. Water is very good at screwing with perception, moreso when the water is dark and brackish and has stuff floating in it.
Lava is another matter, it's not just water, it's molten rock and stuff. So you could argue that it would block line of effect. And even if not, you can't see through it. It's not Kool-Aid Lava they have in the Mario Games.
