If you have a small weeping leak on your freshwater system, it can slowly flood down and collect in the strangest places until it reaches the tip over point where it finally works its way to the bilge. Below the water tanks, and other areas of the boat that are near impossible to clean suddenly getting a slow trickle of water over a course of days push years of accumulated gunk downhill to the bilge.
When you left the boat, was your water pressure breaker turned off? Have your water tank levels dropped when you were away from the boat? We had a tiny crack on the hose where it attaches to the barb at the cold water inlet to the electric water heater.. It was leaking only a litre or so every other day, but once I replaced the hose and barb/tank fitting we were drip dry again.
Take a very close look around your fresh water manifold with some paper towels, the water system on and pressurized, all tank valves open, all tanks full, and check carefully for leaks. You may be simply pumping fresh water from your tanks into the bilge and picking up years of crud and moving it into the bilge. If it was a salt water leak, I expect the stench would be over powering, hence why I'm guessing its a fresh water issue.
The other place to check are your shower sump boxes, (we switched ours to zero maintenance Whale Grey Water IC's), and all raw water sources, (heads, air con, refrigeration, etc), carefully check all the thru-hulls again looking for any trace amount of moisture.
My wise old boat mechanic told me the best bilge cleaner is simply yellow sunlight dish detergent and hot water. It works very well for pennies on the dollar versus expensive bilge cleaners and is non-corrosive to your keel bolts. Just add the soap to the hot water unless you want bubbles everywhere. I use this to tackle the big jobs, and often get everything spotless. However if I need to spot clean afterwards, then I'll bring out the heavy duty cleaners.
Finally if you have any Zaal No Flex Digestor, add a couple of tablespoons to bilge next time you leave the boat unattended, after everything is clean. Zaal breaks down organic material and is harmless to metals. (Product is used to clean hoses and holding tank issues.) If any more black coloured water ends up in the bilge, the Zaal will make clean up easier at least.
