The terrible water quality at Avalon is a decades-old problem reported annually with the release of local beach quality "report cards." The other beach that consistently receives an "F" is inner Cabrillo Beach in L.A. Harbor. They've even tried wholesale sand replacement at Cabrillo with little improvement.
But back to Avalon, visiting boaters have been arbitrarily blamed for this pollution as far back as I can remember. Avalon started a toilet dye program back in the 70's (I think, it was a long, long time ago) where renting a mooring even for a single night meant the Harbor Patrol would board your boat and place fluorescent dye in the head. Any discharge during your stay and you were banned for a year. The result was any sewage discharge that may have happened previously dropped to zero and I repeat, this has been the case for decades.
Yet the pollution remains. It's not as easy to blame the boaters anymore and for that reason alone I'm glad the dye program continues.