You're in luck, 'cause there are actually rules in Pathfinder for cave-ins and collapses:
Characters in the bury zone of a cave-in take 8d6 points of damage, or
half that amount if they make a DC 15 Reflex save. They are
subsequently buried. Characters in the slide zone take 3d6 points of
damage, or no damage at all if they make a DC 15 Reflex save.
Characters in the slide zone who fail their saves are buried.
Characters take 1d6 points of nonlethal damage per minute while
buried. If such a character falls unconscious, he must make a DC 15
Constitution check each minute. If it fails, he takes 1d6 points of
lethal damage each minute until freed or dead.
The given CR for this sort of environmental hazard is 8, but I'm sure you'll be able to scale it up or down, depending on the party level and your intended deadliness of the encounter :-)
Edit:
Going deeper, as required by Eric B :)
On escaping the collapse, let me keep quoting the paragraph I linked to:
Characters who aren't buried can dig out their friends. In 1 minute,
using only her hands, a character can clear rocks and debris equal to
five times her heavy load limit. The amount of loose stone that fills
a 5-foot-by-5-foot area weighs 1 ton (2,000 pounds). Armed with an
appropriate tool, such as a pick, crowbar, or shovel, a digger can
clear loose stone twice as quickly as by hand. A buried character can
attempt to free himself with a DC 25 Strength check.
But how does the underwater situation come in to play? Apart from drowning, we have:
Digging people out: Because water is denser than air, objects submerged in water will have higher buoyancy than when in air. Thus moving rubble and rocks should be easier under water. However, unless our heroes are affected by freedom of movement or similar enhancements, movement is down to one quarter (assuming successful swim checks). Right off the bat, I'd say moving loose rocks underwater can be done at roughly the same speed as above water. Few large rocks would decrease the time, and a huge pile of rubble would probably take quite a bit longer to move under water than above.
Freeing yourself: Because stuff is easier to mover under water, I'd give the submerged character a +5 bonus on the strength check to free himself.
Damage from the collapse: Since damage dealt underwater is halved, I'd apply the same 50% discount to damage from falling rocks.
Pre-warning - I have little experience as a DM dealing with difficult players, but I'm getting pretty used to dealing with difficult tables in general.
A couple of things we found really handy for our horde of uncooperative players:
Talk it out / Remind him
You said in the comments that:
I have talked to him about it before. He seems understanding until a situation occurs where it basically sets it off
So he may just need a gentle, at table reminder about the discussion you've had. A simple prod in the right direction might be all he needs to cool his head. DnD can get pretty intense at times, and it could just simply slip his mind as he gets into it.
Players really getting into your campaign is what you want as a DM, as long as they're getting into in good spirit.
Is the table okay with this behavior?
Is it just you that's bothered by this? How your table reacts to his behavior could also dictate how you handle it.
During our romps with difficult players, one player refused to cooperate with the DM to the point we almost had to kick him out. But the DM pulled me aside, and asked me to respond to every that player said as in character.
If your brother is heavily into role playing, responding in-kind and keeping it to your characters may help stem the OOC poor behavior.
I.E - If he's complaining about the Gods not lending a hand, a NPC (or other player) could take that at face value. "[Gods Name Here] wouldn't care about a single [town/city/country/]! Our lifes are nothing compared to the grand scheme of things. The immortal plane is beyond our understanding..."
If all else fails, are you guys that right group for him?
You also said that:
He generally seems much kinder to other dms, doesn't have the remarks or throws tantrums to them. (He also is my older brother)
So it could very much be as simple as -Younger brother has to do it my way rawr- or that the tables play-style and campaign just doesn't fit him.
Saying that you play to his level, but then having a level 15 player challenge a lv 20 NPC, says to me that maybe he doesn't want that much of a challenge.
He could be looking for something a bit more cruisy, or maybe he just really really wanted to play pirate captain.
But either way, if you can't find a middle ground with him, maybe have another look to see if he matches your table. It could be as simple as a few small tweaks to the campaign to keep everyone happy.
Best Answer
There are no special rules for how magic electricity interacts with water. The surface of the water acts as cover for those submerged, which prevents targeting them entirely. If someone’s partially above the water, they can be targeted normally, with no special consideration due to the water.
This is actually a fairly reasonable approximation of reality, consistent with the limits of the abstraction thresholds of d20.
Ultimately, the danger of being in water during a thunderstorm is that it increases the likelihood that a natural lightning bolt will affect you. It increases the chance of a direct hit, and it increases the effect of a near miss. That is, assuming you are on, or very near, the surface of the water, because that’s where humans generally are. The effects of a lightning strike do not penetrate very far into a body of water: 20 feet, maybe. So being deeper than that provides protection from lightning (precisely as the rules suggest). But if you are on the surface, the problems are these:
You are more likely to be poking up from a relatively flat surface, with nothing else around you of similar height. Just your head sticking up won’t make much difference, as a stormy sea almost-certainly has waves at least that tall. But a boat might, and a mast definitely will, make a large difference. Natural lightning is more likely to strike something that’s up higher than its surroundings.
Water will conduct the electricity somewhat; this only matters if the water strikes very close to you, but ultimately being in water means you are facing a greater current from a strike near you than someone standing on dry land at the same distance. The difference is not as large as you would think, though: you do not want to be within 20 feet of a lightning strike under any but the most controlled of circumstances (you’re totally fine within inches of a strike if you’re in a Faraday cage, and fun fact: cars, with their metal bodies, are pretty decent approximations of a Faraday cage, so lightning can strike your car right over your head without affecting you).
Water is going to react to the blast itself in ways that are potentially more serious than the ground. Water will boil, and pressure waves will radiate from strike point both as a result of thunder and of the water boiling (which, really, are pretty much the same thing since thunder itself is caused by superheating the air). Thus concussive force and substantial heat is being thrown at your body.
What being in water does not do is change what happens if a lightning bolt hits you, rather than near you. It makes that marginally more likely (but a boat or mast would be massively more significant than just floating in the water), but once it has already happened, it doesn’t really matter where you are. The current and heat and concussions applied to your body are going to be quite similar (and near-certainly fatal) in both cases.
And the reason that all of this is irrelevant is because this is below the abstraction threshold of d20: it happily ignores all of this, and does so consistently:
Lightning bolt is a magic spell, and it objectively does not behave the way regular electricity does. It does not follow the path of least resistance. If it did, and created a large potential at the caster’s fingertips, the lightning would not arc out an enemy, it would quite happily take a path of vastly lower resistance and travel up the caster’s arms, through their chest (probably causing cardiac arrest), down their legs, and into the ground. This, obviously, is not what happens nor what anyone casting the spell wants to happen.
As a result, neither your height relative to your surroundings nor the relative conductivity of your surroundings matter. Thus being in water doesn’t make you more vulnerable to lightning bolt for the exact same reason that having a lightning rod doesn’t protect you from lightning bolt: the magic is forcing the electricity to move in ways it would not naturally.
Lightning bolt only does electricity damage. There is no risk of deafness due to thunder, there is no risk of burns (fire damage?) due to the intense heat, there is no risk of damage from concussive force. Why? Magic. Or because the system is an abstraction that simplifies reality to make it playable. Thus, the fact that a lightning bolt boils water, can create fairly intense pressure waves, and so on, just doesn’t apply to lightning bolt. That eliminates a lot of the increased risk of being in water when lightning strikes.
Lightning bolt deals half damage on a Reflex save, and being in water doesn’t affect one’s reflexes (either through Reflex saves or touch AC). One might expect that it does, but it doesn’t. This is true for anything and everything that might affect dodging or moving out of the say. So lightning bolt is consistent with everything else that allows you to (partially) get out of the way: being in water does not affect things. Even assuming magic electricity that didn’t cause side effects, per the last bullet point, one might expect water to increase the amount of current flowing through someone due to a nearby lightning strike (though the difference is not as large as you would imagine), but this does not happen and that is not surprising because the reason you might expect that is because of the rules that natural electricity obeys. But the magic electricity of lightning bolt does not do that, and in fact the spell would be useless if it did.