If you're referring to the two the unions that have rubber hoses attached that are going up and over the cam cover?
These are coolant in/out feed for the cylinder head. The cooling system isn't directly connected, so it's very unlikely this water is from the cooling system, what colour is it, does it feel waxy and how much of it is there?
What often happens is owners/stealers reconnect the the drain/breather hoses incorrectly, one being the filler cap drain hose!
The other ways are, crab to air box inner rubbers, cylinders 2- 3 not seating correctly after being removed allowing rain water in, these can be a bit of a pain to fit, some kind of modification to the airbox, they drill them to get more sound or in the vain hope of more power, blocked crankcase breather.
They're others but these are kinda terminal and very unlikely, look for the simple first.