Hey Ross,
My Kohler 6EOD is a 6KW diesel and it is cooled with a closed loop and heat exchanger versus directly with raw water. So, I am betting yours is the same, even if you are in fresh water. And, if that is the case, I'm really betting on it being a xyz-glycol/water mix. Doing otherwise would just be unusual (and, as I mentioned, in my world, worthy of a cooling system flush and correction).
On your way to the boat what I'd recommend you stop by an auto parts store or Wal-Mart and get an antifreeze tester. They usually cost $4-$9. Something like this:
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https://www.walmart.com/ip/TESTER-COOLANT-PRESTONE/16817506
Then, once on the boat, I'd pull the cap off of the cooling header tank and look at the inside of the cap and the inside of the neck. Then, I'd put my finger or the corner of a clean shop towel into the tank to get into the fluid. See if there is any oily or milky residue. Oil is lighter than water, so if it gets into the coolant, it'll find its way to the top. Maybe if coolant was getting into the oil, oil was getting into the coolant. If you find oil in the coolant, well, that'll be a big hint (the opposite doesn't disprove anything, though).
The next thing I'd do is give the coolant a good smell. Does it smell like water or antifreeze (or antifree-water mix)? After that, I'd check the coolant with the tester. It basically measures the density of the fluid and can give you a good idea if it is water, coolant, or a mix. It'll also let you see the color. Is it clear like water? Deeply colored like antifreeze? Or lightly colored like a mix?
With luck, your nose, your eyes, and the needle will give a similar (or, at the least, not inconsistent) indication. If you want to be a scientist, you can even send a coolant sample out to be tested, just like the oil. Ultimately, if you've got glycol in the coolant (And, I think you really should), but not in the oil -- I really don't think the coolant system is leaking into the oil.
If you find that your cooling system truly has only water, that's not much help in narrowing things down. So, for the sake of conversation (and, because I think it more likely), let's assume that the cooling system has some glycol -- and your oil sample shows none (as I understand is the case). The question becomes, how can raw water get into the oil?
-- One possibility is that it was over-cranked when starting. In a marine generator if the engine won't start and one keeps trying, the raw water pump can push water through the heat exchanger into the exhaust, and then let it fall back into the motor This is actually a pretty dangerous condition, because it can get into the cylinder and cause a hydrolock with damage like bend rods or much worse. Basically, unlike a fuel-air mix, the cylinders can't compress water, so if the generator starts and it tries, things bend and break. (If a genset won't start after a short attempt, close the intake seacock, until it does...)
-- Another situation that can cause a hydrolock in an aft-exhaust genset is cruising without the genset running. If one backs down or gets hit with following seas, without the positive pressure from exhaust, it is possible for water to get forced up the exhaust and for the same thing to happen. (This is why I always cruise with my genset on and had the exhaust and elbow raised higher.) The same can happen with side exhaust from excessive rocking side-to-side when moored or anchored. (In a badly designed exhaust, shared with the main(s), the main(s)'s exhaust can also get pushed backward into the genset).
-- Another possibility is that a human was intending to top off the coolant -- and dumped it into the valve cover cap, instead. It sounds crazy. But, depending upon access, it may be easier to do than it seems. They are often similar-sized push-and-twist caps on top.
-- If the generator has an oil cooler, it could be leaking. I think it unlikely. My last generator didn't have one. And, on my current generator it is a rarely installed option. If you can tell me the model of your generator, I can see if I can find the service or parts manual and look.
As you can probably tell from some of my posts, I am the type that likes to collect all the data first. So, although I'd change that oil and filter repeatedly right away. I'd also have sent it off for analysis (as you did), analyze the coolant (sending it out, if needed), think carefully about the usage and service history for clues (hard start? following seas while off? Recent fill with coolant?) and look carefully for signs of raw water backing up, rust, etc.
At any rate, if you post the model of generator, I can google around and see if I can find the service and/or parts manuals, and see if there is likely an oil cooler or not.
But, I think the absence of glycol in the oil will turn out to be a big clue.
Cheers!
-Greg