I bought a boat, way back when, where the engine bay was just covered by a tarp. The carburetor was left without a flame arrestor and a lot of water went through it into the engine. So it is possible that the water came from rain, just not hugely likely unless stored really poorly.
Does the motor turn over? Does it run? Have you pulled the plugs and looked into the cylinders with a flashlight through the plug holes? Compression test?
As Scott said, it is also very possible the motor was not properly drained before winter and the block cracked when it got cold enough. When he says do a pressure test, that is of the cooling system. A little bit harder than it sounds in that your motor probably has fresh water cooling, meaning the outdrive pumps lake/river water into the motor and as it is used for cooling it is dumped into the exhaust to get rid of heat and to cool the exhaust as well. The system is not pressurized, it is 'open'. To pressure test it you have to cap off the exits and apply a small amount of pressure to the cooling system and listen for leaks. I always figured the easiest way to do that on a 4 cylinder engine was to pull the elbow off the top of the exhaust manifold and make a cap to fit in its place. Then pull the intake line going into the thermostat from the outdrive and pressure from there.
Not a lot of difference between a marine engine and a car engine as far as how they work or how you work on them. Just a few parts that are different to account for being mounted inside a fiberglass bucket and run under full load from idle to top speed. You'll get the hang of things quickly.