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Fresh water tank slime
What you have is a mold/mildew contamination.
What you have to do is get in there and mechanically scrub the system (replace hoses if stained brown, etc.) The mechanical removal of debris will lessen chances of reinfection; dead cells and stunned spores, etc. left in the system will provide nutrients for further infection. Some of these species are EXTREMELY toxic to humans, especially if the spores are breathed-in. WEAR rubber gloves, goggles and at least a dust mask when cleaning such bioburden from the tankage !!!!! That the tanks are fouled also suggests that the boat has a LOT of infection under the hidden walls, floor boards, etc. The vector of contamination isnt city water but the TANK VENT: sucks in spores as you draw down the water. .... Clean or REPLACE the tank vent line. Once the system is cleaned I suggest that you wrap the entrance of the vent with a big wad of sterile gauze, keep it dry and change yearly.
Then go after all the "BLACK SLIME" that lives in all the dark places on your boat, use Chlorox spray, etc. and be SURE to wear the protection listed above. When closing the boat for long periods of time consider to place in loose paraformaldehyde crystals to kill more of the mold/mildew. Vent the boat to allow the para-F gas to vent out BEFORE entering.
Once you mechanically remove the tank debris, shock sanitize the whole system: tanks lines, faucets, pumps ..... and VENT with a STRONG solution of Chlorox.
If youre not "afraid of chemicals and KNOW how to use them" a caustic dilute solution of Sodium Hydroxide that is allowed to soak for period of time will dissolve the bio debris remaining after mechanical scrubbing. The system is then scrupously flushed with water, then neutralized with a mild acid (vinegar) ..... then Shock sanitize with Chlorox. Dont use caustics if you dont know how to use them or if you dont understand the harm caustics can cause or the personal protection needed.
After the system is cleaned add fresh water and add enough Chlorox.... so that you get just the faintest perceptable smell of Chlorox in the outlet water to keep the ''critters'' stunned and unable to reproduce. Dont follow ''recipies'' ... just use your nose to get the "faintest possible chlorine smell" from the output water. Adding more that this amount is harmful- many authorities suggest that excessive chlorination of water can lead to cancer, and other metabolic disorders etc.
The use of carbon filters installed in the tankagae lines, etc. is STRONGLY NOT recommended as the carbon is a nutrient source for bacteria etc. PLUS it will adsorb the active free chlorine used for maintenance. If you MUST use carbon for odor removal etc., use it ONLY on the hose that you use to fill the tank.
Hope this helps.