Water in engine

[tobes]

My son bought this Honda Ballade (pop-up) with aftermarket turbo installed.He is busy preparing it for roadworthy,but it was standing for some time outdoors since the last time we took it out on the road.Yesterday he started it up and let it idle a bit.This morning he found water in the intake and apparently it went right through to the pistons.He and his friend dried everything out and upon starting a puddle of water came out of the exhaust (cut off halfway).I was not present when all this happened,but they checked the intercooler and it looked like it was not leaking.
Question:Other possible causes and how does it happen that water ends up in the exhaust?
My knowledge on turbos is extremely limited.

[tobes]

Fixed up.Had a look.Looks like rainwater entering through a cone filter.Filter was installed at an awkward place in the engine bay.