In your engine compartment, look down along the forward bulkhead were it meets the hull bottom, at the outer most stringers and see if you have drain holes. Mine are directly in front of my batteries. Those are the drain holes for the cockpit floor drains.

Try Snaking it.

I have no idea where the water goes either. When i wash the floor in mine i have checked both the engine compartment and under the step in the cabin but i never see water. Now when i pull it out of the driveway and start heading down the road the automatic buildge under my step in the cabin starts shooting water out. So it must sit somewhere till it gets at the rite angle to get to the buildge.

Figure it out sooner than later and get it dried out. If it's sitting under or around the fuel tank that will be your biggest nightmare.

It's really the only unknown I have with my boat. If that tank goes man it's gonna be borderline not worth fixing.

Run a dehumidifier under a tight plastic cover if you can. I've always been curious as to how much cockpit would have to be cut out to do a new fuel tank. It's under the bench seat too with molded base.

NO FUN.

Wonder how you figure out if you have water in the fuel tank area? I bought my boat in september and dummy me didn't lift up the carpet when I was inspecting it. Someone must have dropped something heavy in the floor because my floor is spiderwebbed cracked pretty bad in the back area. I don't think it is bad enough to leak water but the thought is still in the back of my head... Thought about rolling gelcoat in my floor just in case and always leave my carpet in.

I don't have a definitive answer for you. My first thought is to use a good quality video scope and fish around with panel off. Also, go up the drain holes in the bilge as far as you can see in the center. Try to get it under the tank and look for standing water. The easiest way to dry it out is either storing in the desert or dehumidifier.

I've seen LOTS of fuel tanks that have eaten through simply because of water standing.. Even fresh water.. Center consoles are easy to hack up and fix. Small boats like mine are a nightmare and taking a sawzall to it is gutwrenching.

Personally, for me, it's so scarry I'm going to stop talking about it and turn my head. I say that only because of the work and damage I would have to do to the boat to fix it. And it might not ever look as nice after the replacement.

Not trying to be a fear monger here but if you just start looking closely at the boat and ask yourself "how do I replace fuel tank" you will see what I mean. If you have a junkie looking boat it won't matter. Mine is almost as pretty as the wife.

You have to cut the floor out fix the tank and reglass the floor. Then put a removeable carpet over it, or re-gel it, or both/ Fountain Performance Marine can do this as well as help you diagnose your problem. I would contact them above and beyond anyone else. They have been there before.
hope this helps.

My 32' SC drains the water from the cockpit floor out the engine compartment hull sides via hoses and through hull fittings with one way check valves.
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My boat is in great shape for a 98. I know exactly what would have to be done so I would deff take it somewhere... So Hopefully I don't have any standing water either... My comment was a big "IF." Also going to stick to not washing the inside with a water hose... First time i washed it like that it was sitting slightly down hill and it took FOREVER to dry out the cabin and side storeage. Live and learn from your mistakes...

Fountains sit nose low on trailers. Gotta get that nose up high if you are going to turn a hose on the inside of it