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I have my concerns about water quality in the Chesapeake and other estuaries as well.
My own anecdotal evidence is that the water quality near shore is definitely suspect as the water is very turbid (lots of suspended particulates) which is consistent with most of the rivers feeding the Chessy from the western shore. Rivers tend to be turbid.
This last spring we crossed the mid-Chesapeake to St. Michaels using the spinnaker. We also trailed lines from the stern and swam in what seemed like very clear, salty water not far from Bloody Point Light.
In high summer there will be jelly fish of different varieties so you ought to be careful no matter where you choose to swim.
While I agree that you should be concerned about the water quality I think your concerns are a little overblown. There is some really 'fresh' ocean water out there in the middle of the bay and then there is river water and the two do mix.
My guess is that the southern Chessy region has saltier and better quality water as it gets flushed out more often. The mid Chessy is pretty good in the deeper channels and the upper Chessy has the Susquehanna River flowing into it which is a problem river.
The Rappahannock River is allegedly one of the cleanest rivers on the western shore, due to the lack of historical commercial uses in its drainage area. Apparently there are still a breeding population of Sturgeon in the James River.
The oysters were the blue crabs of yesteryear and were over fished until they found a way to market blue crabs, which became all the rage almost 100 years ago. Now the blue crabs are also over harvested. The 'bay' is under a lot of stress but I would not turn my back on it just yet or the folks that make a living from working the 'bay'.
300 years ago the Chessy was as clear as a bell all over and covered in Oysters, Mussels and other filter feeders. 300 years later it is just not quite the same place, but it is still a great place to sail. And so we do, and we swim and sometimes shower afterward.
"The cure for anything is salt water~ sweat, tears, or the sea." ~Isak Denesen
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