"I have both fresh and a salt water tanks "
I've never heard of having a salt water tank on the boat, it sounds like you have two fresh water tanks and one of them has simply become contaminated.
Like tj said, it is not uncommon on smaller less expensive boats to pull a hose into the cabin and fill the tank directly. You need to access both tanks, and see what filler plates or hoses are on them. If there are no filler hoses...there's no fill from the deck.
Check the lines running out from the tanks, usually they are joined by a "t' or "y" fitting that runs to the galley & such.
Salt water tankage on a 29' boat? That would be *most* unusual.