ANNAPOLIS, Md. - "That's big enough to hurt," naturalist John Page Williams said as he pulled his 17-foot Boston Whaler alongside a tree trunk floating in the Chesapeake Bay.
Three weeks after the flooded Susquehanna River sent millions of tons of dirt and debris from Pennsylvania into the nation's largest estuary, the water that had been churned chocolate brown was returning to green and most, but not all, of the trash had floated to the shore or sunk.
With less threat of boat-wrecking flotsam, Williams from the Chesapeake Bay Foundation and scientists throughout the region are taking to the water to study the less visible, long-term impacts of the flooding on the already suffering bay.
Just as the rush of water devastated communities along the Susquehanna's banks, it shocked the complex ecosystem at the river's brackish tail.
On Wednesday afternoon, Williams leaned over a sonar display and poked at the bottom part of the screen, which reflected a blank expanse in the deepest part of the bay under his boat. Dots indicating fish were
pinched near the surface and nothing living lingered below.
"You see this? That's what a dead zone looks like," he said, floating south of a massive pylon for the Chesapeake Bay Bridge.
He had just pulled an oxygen reading from 14 meters down of 2.4 milligrams per liter. "Anything under five is uncomfortable for, say, a rockfish," he said. "Below three is borderline lethal."
Dead zones are the biggest challenge to the health of the bay. They are oxygen-deprived areas underwater that kill anything that cannot swim out of them and stress the fish and crabs that can. They are caused by the nutrients - phosphorous and nitrogen - that run off fertilized fields, over roadways and from overburdened storm sewers every time it rains throughout the bay's 64,000-square-mile watershed, including 21,000 square miles of the Susquehanna River basin.
Algae feast on the fertilizer, bloom and die, then suck the air out of the water as they decompose.
Dead zones typically stretch throughout the bay in the spring and summer, but scientists are finding signs of a late season dead zone spurred by the surge of nutrients and decomposing flood debris on the bottom. They are also studying the chances of a worse than normal dead zone next year.
If it arrives, it will come on the heels of one of the worst dead zones ever recorded in the bay this summer, which formed in part because a wet spring delivered tons of nutrient pollution with the water.
"By June of this year, Pennsylvania discharged through the Susquehanna River as much pollution to the Chesapeake Bay as it does during a normal year," said Harry L. Campbell III, a Pennsylvania-based senior scientist for the Chesapeake Bay Foundation.
The assault of pollution brought by the recent flooding only capped that massive load.
The floodwaters also brought other hazards. Hundreds of billions of gallons of fresh water changed the bay's brackish balance between salt and fresh throughout the tidal basin.
When flood gates were opened at the Conowingo Dam five miles south of the Pennsylvania border, every tree, propane tank and port-a-potty trapped against them rushed with the water out into the bay.
The U.S. Geological Survey estimated that the force of the river also scoured 4 million tons of sediment from behind the dam, an accumulation that had been deposited there over years. That is the equivalent of 400,000 dump trucks dropping loads of dirt directly into the Susquehanna River just north of the Chesapeake, Campbell said.
The number does not account for the tons of sediment that was scraped from stream bottoms and flooded fields all along the Susquehanna's path. Scientists are still working to determine that figure.
"Not only do you get the sediment that just came off the fields in Pennsylvania, but you get the sediment that ran off years ago," Chesapeake Bay Foundation media relations director John Surrick said.
In the days after the flood, the plumes of sediment were visible from space.
The dirt - mainly fine clay - harms the bay in many ways. When it settles on the bottom, it smothers underwater grasses that provide habitat for fish, suffocates the already depleted oysters and covers the hard surface necessary for new oyster growth with soft muck referred to locally as "black mayonnaise."
Dead or smothered grasses cannot add more oxygen to the bay and they don't hold the silt already on the bottom in place, causing more sediment to mix with the water.
After flooding from Hurricane Agnes caused the highest-ever recorded flows from the Susquehanna into the bay in 1972, "it took, years and years and years for the underwater grasses to come back," said Tom Parham, director of tidewater ecosystem assessment for the Maryland Department of Natural Resources.
Flooding from Tropical Storm Lee will likely have a far less devastating effect, in part because of the late summer timing of the storm after most of the grasses have reproduced and begun to die back for the year. But the force of the water clearly damaged the grasses, especially fresh water species near the mouth of the river. The most recent flooding amounted to the third highest flows ever recorded from the Susquehanna into the bay.
"In lower areas of the bay, we found a lot of pieces of underwater grasses from freshwater species that had gotten blasted down," Parham said. Uprooted grasses formed floating islands tangled with trash after the flood waters rushed through.
In a possible "silver lining," Parham said, some species of grasses that were reproducing at the time of the flood might have had help transporting their seeds to new areas to colonize.
The flooding might also have had another silver lining.
Such catastrophic events tend to "remind us of the often forgotten connectivity that we as Pennsylvanians have to the rivers and streams in our own backyards and our connection to the Chesapeake Bay," Campbell said.
Williams calls the bay the tidal Susquehanna, a geologically accurate name that also reinforces the bay's connection to the communities along the main river that feeds it. To visitors from Pennsylvania, he calls the Susquehanna "your river." As in, the flooding deposited in the bay "just windrows of trash and 40-foot trees. That's how big your river is."
At one point during his boat tour, Williams gestured out and said, "This is you, Scranton."
Campbell agreed.
"Quite frankly, the Chesapeake Bay is simply a mirror reflecting back to us how we treat the land and the thousands of miles of tributaries in people's backyards," he said.
The routine, daily pollution dumped into tributaries is by far the biggest obstacle to restoring the bay's health, he said.
Parham said scientists have nowhere near a clean picture of what the most recent flood's impacts will be on the bay and its ecosystem.
"This is just an ongoing, developing story," he said. "As the weeks and months go by we're going to start to have a better idea."
Informed speculation makes it clear to researchers that the rush of water will reverberate in some manner, he added.
"Knowing the way these creatures operate, they were in for a tough little ride." Highest recorded flows from the Susquehanna River to the Chesapeake Bay:
June 1972: 1,130,000 cubic feet/second
January 1996: 909,000 cubic feet/second
September 2011: 778,000 cubic feet/second
Amount of sediment scoured into the bay from the Conowingo, Md. Dam: 4 million tons
Source: U.S. Geological Survey