if you have a vertical muffler on your tractor and water is getting into your cylinders, thats bad stuff, especially if your engine sat up most of the winter. reason being, that water will wind up rusting internal parts on your engine, which have very close tolerances, ie piston to cylinder clearances ect. not to mention, if you get pitting in your cylinder walls, you could wind up with broken rings, compression loss ect and have to wind up replacing the sleeves and pistons, and then there is the issue of your combustion chamber filling with water and corroding injector nozzle tips, glow plugs ect. water inside your engine is an all around bad deal. if you are pretty sure its getting in through your exhaust, do what ever you can to keep that water out, cover the exhaust with a bucket, what ever just keep out the water.one question , did you check your engine oil? if so what does it look like? is it grey or milky colored? thats a sure sign of water intrusion. then you just need to narrow down where its coming from. could be the exhaust, especially if you dont have a cover on your exhaust pipe. or it could be coolant from the engine block, which could mean leaking or blown head gasket, crack in the cooling jacket of the block ect. if you are unsure of whether the water came from the exhaust or the cooling jacket, you can pressure test your cooling system with a tester (available at most auto parts stores) or when you get it running, you have an overheat problem. one thing i do, just to kind of keep things easy is start my tractor atleast once a month during the off season and let it run for 15 or 20 minutes. just my 2 cents, hope it helps