Organic Pollution

The EPA, trying to figure out why the Chesapeake Bay ecosystem continues to decline, has focused over the past few years on animal manure. They have handed out big fines to chicken farmers on the Eastern Shore who don't properly handle the mountains of manure produced by their birds. And now, according to the NY Times, they have turned their attention to Amish and Mennonite farmers in Pennsylvania. Plain sect farmers use the old European mixed farming system, in which manure from animal barns and pens is stockpiled, left to rot for about a year, and then spread on fields as fertilizer. Modern dairy farmers generally store their manure in special concrete pens surrounded by plastic fences, which limits runoff. But many Amish farmers pile it in places whence nitrates are leaching into the ground and running off into nearby streams. There are organic, traditional ways to controls this -- put the manure on impermeable soil and surround it with an earthen berm, for example -- and the EPA is trying to get plain sect farmers to use these measures. Since they have a religious objection to taking advice from the government, and refuse to apply for government grants they could easily get to make improvements, this is proving tricky. (Take note, Tea Partiers -- that is how real anti-government conservatives act.)

My question about this is historical. Everyone agrees that in the early 1800s, the bay was still healthy -- that was when the famous oyster industry really got going. But in the early 1800s there was a lot more farming in the watershed than there is now, all of it using the same mixed farming techniques that the EPA thinks are a problem. Why is it a problem now?

Was the bay so damaged during the era of over-exploitation and industrial pollution, 1870 to 1970 or so, that it lacks the natural strength to handle problems it once managed with ease? Perhaps when there were billions of oysters in the bay, their combines filtering power kept the water clean. Or is the real problem something that did not exist in 1820, like the chemical herbicides used in no-till farming, or birth control pills, or some other weird thing we put in the water?