From streams whose banks were shredded by floodwaters in New York, to a cascade of chocolate-brown water that spread halfway down the Chesapeake, severe late summer weather delivered a heavy blow to the Bay and its watershed.

In a one-two punch, Hurricane Irene, which hit the eastern portion of the watershed Aug. 27-28, and Tropical Storm Lee, which hit two weeks later, dumped more than 2 feet of rain in a two-week period on some parts of the watershed.

In places like Bradford County, in northern Pennsylvania, resulting floodwaters scoured out huge sections of land. "We have been on sites where farmers have lost 2 or 3 acres to 8 feet deep," said Mike Lovegreen, manager of the Bradford County Conservation District. "That's a lot of material headed toward the Chesapeake Bay."

Hundreds of miles downstream, that dirt - and sediment originating from countless other sites - left a plume the color of café au lait that stretched from the Susquehanna River to the Potomac River in the weeks after the storms. The water was filled with debris: mats of uprooted underwater plants, trees, tree limbs, tires, traffic cones, uncountable numbers of plastic water bottles and assorted trash.

Mixed with the debris and mud were untold gallons of raw sewage from flooded wastewater treatment plants and broken sewer pipes.

Many areas were unsafe for boating; those who ventured out reported having to push aside debris in order to move.

It will take months for scientists to fully assess the storms' impact, but it's certain they took a toll on water quality.

"It is certainly going to have a significant impact," said Bruce Michael, director of the Maryland Department of Natural Resources' Resource Assessment Service. "When we put out the [Bay health] report card for 2011, most of our water quality parameters are going to take a hit."

But scientists held out hope that the storms' late-summer arrival would blunt their impact on fish, shellfish and plants that call the Bay home. The storms came well after most fish species had spawned and after the growing season for underwater grasses.

Nonetheless, the magnitude of the storms makes it possible that ripple effects - such as worse than normal water quality - could be felt into next year. And some bottom dwellers, including oysters, are still vulnerable to being silted over by the huge amounts of mud flushed into the Bay.

One thing is clear, many scientists said: This year's weather is a stark reminder that the Chesapeake, which has lost much of its natural buffer against storms -wetlands, wooded riparian zones and oyster-filtering capacity - remains in such a fragile state that Mother Nature can easily trump management efforts.

And the number of those events, and their severity, could increase in the future.

Record flows before storms

Even before Irene and Lee, weather played havoc with the Bay.

An extreme cold snap early in the year was blamed for killing 31 percent of the Bay's adult blue crabs.

March through May had the highest three-month average flow ever recorded from the Susquehanna River, the Bay's largest tributary. By June, that freshwater had driven salinity levels at many Maryland monitoring stations to record lows for the month.

Those rain-driven flows also washed large amounts of nutrients into streams. In March, the U.S. Geological Survey estimated that 1.3 million pounds of nitrogen a day was reaching in the Bay from the Susquehanna, nearly twice the average for the month. By late spring, the USGS estimated the Susquehanna had surpassed the roughly 115 million pounds of nitrogen it delivers to the Bay in an average year.

The combination of high riverflows and high-nutrient loads established conditions that led to a record oxygen-starved dead zone during parts of the summer. (See "About the 'dead zone,'" on page 21.) In early June, the Maryland DNR reported that 33 percent of its portion of the Bay was either hypoxic (less than 2 milligrams of oxygen per liter of water) or anoxic (less than 0.2 mg/l). In late July, the number was 39.4 percent. Both were the worst observations ever seen during the month.

Nutrients weren't the only things moved around by the high flows. Northern snakehead fish turned up in the Nanticoke, the Rhode River, St. Jerome's Creek near the mouth of the Potomac, and a tributary to the Patuxent.

The nonnative freshwater predators had been established in the Potomac River for several years, and the high, spring flows and reduced salinities may have allowed them to migrate into other tributaries. "It's starting to appear that they may have made a beachhead outside of the Potomac, which is obviously bad news," said Steve Minkkinen, who heads the U.S. Fish and Wildlife Service's Maryland Fisheries Resource Office.

Minkkinen noted that it's also "very likely that blue catfish made an egress out of the Potomac."

Hot summer compounded woes

The impact of high flows and nutrients were compounded by an unusually hot summer that helped fuel algae growth. The National Oceanic and Atmospheric Administration said that in July, Reagan National Airport in Washington, DC, had its warmest single calendar month on record, with 84.5 degrees. In July, many monitoring stations in the Bay were reporting their highest ever temperature readings.

"It's just been a wild year," said Mike Naylor, head of the Maryland DNR Shellfish Division. "No year is ever normal, but this year is even less normal than normal."

Hot surface temperatures and large areas of oxygen-starved water is bad news for some fish, such as striped bass, which try to avoid stress caused by heat by swimming into deep water only to find those areas off-limits because of the lack of oxygen.

On the Potomac, hot sunny conditions during the summer also spurred on a dense, 18-mile-long bloom of Microcystis, a toxin-forming algae species that persisted for weeks. Agencies warned people to avoid contact with the water.

Scientists worry that the hot temperatures may have also set back eelgrass, a critical underwater grass species in the lower Bay. High temperatures can kill eelgrass, especially when combined with poor water clarity, which limits its ability to get energy from sunlight, causing it to use up energy reserves.

Eelgrass acreage, which had already been hard hit in recent years, "are really going to be down quite a bit," said Bob Orth, an underwater grass expert with the Virginia Institute of Marine Science.

But not all of the news was bad. New grass beds were seen in many areas, especially low salinity waters - including the first underwater grass bed documented in the James River in recent years, Orth said.

Irene brought some benefits

Conditions changed rapidly when Hurricane Irene came up the East Coast on Aug. 27, striking coastal areas of Virginia and the Delmarva Peninsula. It brought damaging winds and heavy rains to parts of tidewater Virginia and the Eastern Shore - and more nutrients into the Bay. The Choptank River, where new grassbeds had been observed earlier this year, had its highest flow on record after Irene, topping the U.S. Geological Survey gauge on the river.

Irene had some benefits. Its high winds helped to mix the Bay's water. By late August, the dead zone was gone.

"If we hadn't had Irene, this could have been the worst summer on record as far as the dead zone," the DNR's Michael said. Instead, when June and July figures are averaged with August and September figures, this summer's dead zone will be bad - but probably not the worst - on record.

Winds from Irene also broke up the toxic bloom on the Potomac.

But Irene also brought rain that soaked the soils in much of the watershed. Before they could dry, Tropical Storm Lee moved into the watershed from its landfall on the Gulf Coast.

Heavy rains - a foot or more in some places - quickly ran off soils that were already soaked, causing flooding and widespread damage, particularly in much of the Susquehanna basin.

Flows on the river peaked at 778,000 cubic feet per second on Sept. 9, and 43 of 53 floodgates on the Conowingo Dam were opened to allow water - along with an immense amount of sediment and debris - to escape. The average September river flow is 18,800 cfs.

It was the second highest flow measured at the dam since flows from Tropical Storm Agnes peaked at 1.13 million cfs in 1972. Flows in January 1996, caused in part by an ice blockage upstream, hit 909,000 cfs.

When flows approach and exceed 400,000 cubic feet per second, they also begin eating away at sediment that has built up behind the 100-foot-high dam over the past decades. Flows at the dam, located 10 miles upstream from the Bay, exceeded that threshold for about three days and scoured out an estimated 4 million tons of stored sediment. Still, the USGS estimated that Tropical Storm Agnes scoured about five times more sediment.The sediment scoured from behind the dam also may have contained long-buried chemical contaminants. The USGS is monitoring for contaminants, as well as bacteria and pesticides.

What's not yet known is how much additional sediment came down the river and through the dam. Probably a lot. While the amount of nitrogen transported downstream is generally related to overall water flow, the amount of sediment and phosphorus - which often binds to sediment - is related to the strength of the flow.

"The bigger the storm, the more sediment. We know that," said Allen Gellis, a USGS scientist.

Susquehanna Flats hit hard

One concern is the status of the huge grass bed in the Susquehanna Flats. The largest in the Bay, it was in the direct line of the water and mud rushing from the Susquehanna.

The bed survived the event, but many plants were ripped up, and scientists are worried that its size and density could be diminished next year.

"A lot of the [underwater grass] was ripped out of the Susquehanna Flats," Michael said. He and other scientists held out some hope that high flows would distribute seeds and plant material in new places, helping to spur the growth of beds there. But overall, they expect underwater grass acreage to be down sharply next year.

Underwater grass scouring was also noted in upper parts of the tidal Potomac, where some tributaries, such as Difficult Run in Fairfax County, had record flows.

Also of concern was whether sediment would bury beds and seeds for next year's plants. But exactly how thick a mat of sediment was spread across the Upper Bay won't be known for a few weeks.

Biologists were also worried about the storm's impacts on oysters. The damage won't be known until surveys begin this fall, but Naylor of the DNR said the oysters most at risk are those in the Upper Bay and on the Western Shore, where salinities are lowest and sediment concentrations highest. "It's ironic because in the last 10 years we've been talking about how those areas have been doing pretty good," he said.

Naylor said he expected the bulk of the state's oyster population, which is located in the lower Eastern Shore, to escape the worst impacts.

Meanwhile, the high flows had caused the Bay to restratify, and by late September, a zone of oxygen-starved water was reforming in deepwater areas from the Bay Bridge to the Patuxent River.

"It certainly is not as extensive as what we saw last summer," Michael said. "The good news is, even though this is setting up, there is certainly plenty of good habitat for fish at this time of year, especially with cooler temperatures on the surface."

Algae blooms anticipated

How much of the water quality effects of Irene and Lee carry into next year probably depends on whether large algae blooms form this fall, said Walt Boynton, longtime Bay researcher with the University of Maryland Center for Environmental Science. That algae would absorb excess nutrients from the storm, die, and sink to the bottom of the Bay.

But with cooling fall temperatures, the decomposition process might not be completed, leaving the nutrients "sitting on the bottom, ready to go next year," Boynton said.

In late September, the Bay was still too murky for algae - which requires sunlight - to form large blooms. But scientists expected that situation to change as sediment began dropping out of the water.

"I fully anticipate that we will get a fall phytoplankton bloom," said Mike Roman, director of the University of Maryland Center for Environmental Science's Horn Point Lab, who was conducing a monitoring cruise through much of the Bay - part of an ongoing project now in its ninth year.

That cruise was part of an unprecedented, coordinated monitoring effort by state, federal and university labs to capture the impact of the storms. New monitoring was added, while schedules for other monitoring activities - such as Roman's trip - were slightly altered to maximize their ability to capture storm data.

Cleanup efforts are often geared toward average or normal conditions - annual nutrient and sediment goals for the Bay are set for "average" hydrologic years. But scientists recognize that extreme events can have disproportionately large impacts on the Bay and its watershed, although such events have not always been well-captured in monitoring efforts.

Understanding them is considered to be especially important because scientists expect the frequency and severity of such events to increase as the region's climate changes.

"We are likely to see these kinds of storms more often in the future," said Rich Batiuk, associate director for science with the EPA Bay Program Office.

The continued impacts of the storm are expected to continue to play out over time. For example, it often takes a long time for finer grains of sediment to become buried, so they may be easily resuspended and contribute to murkier-than-expected water in the Upper Bay next spring.

As those particles that settle to the bottom, they could smother bottom-dwelling organisms - as well as the hard substrates critical for many species.

In some upstream areas with heavy flooding, stream channels and floodplains were destabilized, which could lead to increased erosion in coming years.

In other places, best management practices installed in riparian corridors, such as streambank fencing or forested buffers, were damaged, or in some cases, eliminated. That could also increase future runoff.

In New York, Jim Curatolo, watershed coordinator for the Upper Susquehanna Coalition, which represents conservation districts in southern New York and northern Pennsylvania, said a $120,000 stream restoration project that was created this year was washed away in the floods. Adding to the insult, a sewage pipe just upstream broke and covered the site with sewage.

Many other projects, he summed up, were "toast."

"I think this might be a lost year," he said.

About the 'dead zone'

Wet conditions typically trigger poor water quality in the Chesapeake as rainfall drives increased amounts of nutrients and sediment into rivers. Nutrients fuel increased algae production; when the algae die and sink to the bottom, they are consumed by bacteria in a process that removes oxygen from the water.

In addition to flushing more nutrients into the Bay, strong river flows, especially from the Susquehanna, create a barrier between fresher water on the surface, and heavier saltwater on the bottom. This barrier, known as the pycnocline, can prevent oxygen-starved water on the bottom from mixing with surface waters. As algae on the bottom are consumed by bacteria, oxygen is used up and cannot be replenished, creating a so-called dead zone.

Generally, the greater the freshwater flow into the Bay, the stronger the pycnocline and the greater likelihood that a dead zone will form in deep areas. Sediment core studies show that low-oxygen conditions have long occurred during years with high streamflows, but their size and frequency have increased sharply in the past half-century as nutrient runoff has increased, increasing algae production.