The typical causes of water in a cyl is a leaking exhaust system (exhaust elbow gasket leaking or elbow/manifold rotted through), blown head gaskets, cracked cyl head or block.
You can check for bad exhaust by draining the exhaust system of water and then removing the exhaust elbows, and see if there is water or signs of rust in the bottom of the center exhaust passage. If you find this that's an easy fix, remove the exhaust manifolds test them for leaks by filling with acetone, if they leak replace the manifolds if not they may be re-usable as long as the sealing surface is in good shape. I'd probably just replace the elbows if you don't know how old they are. Use VP gaskets and follow the instructions.
If on the other hand you don't find any sign of water in the exhaust gas passage, then you have to drain water out of the engine and do a cooling system pressure test. If you do a search people on this forum have described how to do it. If it passes this then that's good, if not you have to remove the heads and have them checked for cracks, and check the cyl block for cracks. Usually in a bad overheat the heads will crack but they don't always leak depending on where the cracks were, but the head gaskets will often leak after a bad overheat and cause the same problem (water in a cyl, hydrolock).
I had a similar problem, water in a cyl but no hydrolock, and found the cause from testing (blown head gaskets) I drained the water out of everything, and sprayed fogging oil liberally in the cyls, cranked it over and sprayed again, and then stored it for the winter. I took it apart in the spring and replaced the heads with remanufactured heads and new gaskets/head bolts. Still running well now 3 years later. You gotta get all the water out, I changed the oil 3 times in this process before storing it. Get the water out and oil the cyls. Ideally you would fix it now, but I waited on mine and was able to ressurect the following spring.
