I ran through a big water puddle that was really deep and it made my truck stall after going thru it. It wouldn't start for about an hour and a half. But since then it's been running really rough and reving at random times on it own and sounding like its gonna stall but hasn't yet. And it's been doing this for as little over a week. Did something ruin underneath my truck from getting wet?? What can I do or check to fix this problem

Kind of depends on how fast you hit the puddle. If pretty fast, there's some water laying around from the big splash underneath, shorting out your ignition. Usually, if you just let it dry out, it will be ok. Give it a few hours if it's warm, more if it's not. The best approach to a puddle is SLOW.

All the electrical plugs should be weather pack plugs. this type of water and the low pressure of it, shouldn't get into them. If it was a lot of water, check the air filter. If it is misfiring, check spark plugs wires and or coil boots. which ever you have.

Don't drive thru puddles? Water gets on electrical components causing temporary stall state.

coil if is fitted,earth wiring,

You might want to check the coil, Pull the coil wire from the coil about an inch crank the engine you should see it spark from the coil to the cable, If not you popped your coil

A car will stall when driven through standing water if the ignition system is not watertight. Worn spark plug wires and coil wire, improperly seated spark plug wires, or loose distributor cap are all possibilities.
There is a spray called CRC or some agent that promotes a water drying action can be used to dry out a wet distributor cap and wires. Drying off the electrical components will remove the moisture that is grounding the electrical energy that should normally go directly to the spark plugs.
If car will not restart after stalling from the water splashing as described in the question - and the poor condition of the electrical system is ruled out, some water may have passed through the air intake into the engine and perhaps into the cylinder. If this happens have the car towed to a repair shop where they can remove the water before any further damage results. This condition is not easy to occur but a real deep puddle can set the stage for water to be sucked into the air intake and pass through the filter into the intake and through the valves into the cylinders. This is why you see a Hummer with a snorkel - for wading through deep water.
Read more: http://wiki.answers.com/Q/Why_does_your_car_stall_when_you_drive_through_a_puddle#ixzz1CuKhPDHg

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you have a firing issue .. replace complete spark system plugs wires distributor cap rotor button and coil what happened is you got it wet and coil broke down water got inside distributor cap and messed it up .. you might even have to go as far as to replace the entire distributor

Clean your Throttle body with throttle body cleaner or Deep Creep made by Seafoam. When the carbon and varnish build up in your throttle body get's hot, it gums up the IAC (Idle air control) valve which help moderate your engine's rpm to keep it from stalling.
If the IAC is stuck due to the gum of the carbon and varnish in your throttle body, you have stalling issues which you have described. Start with that and replace your air cleaner filter since your going to clean your throttle body.
Good luck and be safe, thank you for using fixya and post us back.

Does the engine turn fully or not? If not the connecting rods are more than likely twisted to your pistons if he hit the deep puddle at a fast rate of speed. The pressure of the water would of passed through the engine's crack seal producing deadly effects to the engine

I would remove the air box. There is probley water inside of it, causing the engine to constantly **** up the water. Give the battery a good charge.... I assume the car is turning over? Let me know if you need any farther assitance thank you for using fixya.com