Sitting next to his desk, Mike Naylor has a time capsule. It’s a cardboard box filled with black and white pictures.

Every time the Maryland Department of Natural Resources biologist peers at the images, he sees photographic evidence of what might be called the lost grass beds of the Chesapeake.

They reveal an ecological treasure: a Bay filled with thick, underwater meadows that extended hundreds — even thousands — of feet from the shore, providing almost unimaginable amounts of habitat for fish, crabs, ducks and other water-dwellers.

“People that are my age have no recollection of that,” said Naylor, who is 32. “I think a lot of people don’t realize what has been lost.”

Quite a lot, the photos indicate. In river after river, the recently discovered photographs show that only a few decades ago, huge amounts of the ecologically important grass beds existed in areas that harbor only small patches today.

But the photos may be more than pictures of the past. They are being used to help figure out what the Bay of the future should look like. The Chesapeake 2000 Agreement calls for using the historical photos, some of which date to the 1930s, to help set new grass bed restoration goals.

Naylor, as well as researchers at the Virginia Institute of Marine Science, are painstakingly examining hundreds of old photographs — most of which were taken for old agricultural surveys — scanning them into computers, and mapping exactly where grass beds once existed.

The photos will also be an important part of the Bay Program’s efforts to set new Chesapeake cleanup goals. It plans to establish new water quality criteria that would ensure that enough light reaches the bottom for grasses to thrive. The Bay Program will set nutrient and sediment reduction goals that would make sure those — as well as other new water quality criteria under development — are met by 2010.

Submerged aquatic vegetation, or SAV, is considered one of the most important resources of the Chesapeake. The vast underwater meadows provide food and shelter for an array of species. They also help to protect the shoreline from erosion, absorb nutrients and pump oxygen into the water.

But in recent decades, huge increases in the amounts of nutrients and sediment in the water have caused a dramatic die-off. Sediment clouds the water, while nutrients spur algae blooms on the water’s surface, as well as algae growth directly on the leaves of the grasses. All of these block sunlight, which is essential for all plants, including SAV.

In recent years, the total amount of grass beds in the Bay has hovered between 60,000 and 70,000 acres. Everyone agrees that’s only a fraction of what was once present; some suggest there was once 10 times as much. But no one knows for sure. Aerial and ground surveys of Bay grass beds were not made until the 1970s, and annual measurements didn’t begin until 1984. The reviews now under way at DNR and VIMS will provide the first concrete evidence of where the beds were in the recent past.

“As opposed to some scientists saying what we think was there, we have real hard evidence that, in fact, grasses can survive in many of these river systems,” said Rich Batiuk, associate director for science with the EPA’s Bay Program Office, which is funding the review. “These photos provide clear evidence that we can revegetate big sections of the Chesapeake. It is going to take a lot of work, and a lot of nutrient and sediment reductions, but you could see grasses lining many areas of the Bay that are now completely unvegetated.”

The idea of examining old photos for clues about the Bay’s lost grass beds originated with Kent Mountford, former senior scientist with the EPA’s Bay Program Office.

In 1992, one of his neighbors on St. Leonard’s Creek in Maryland, Kathleen McQueen, gave him an aerial photo of her property that had been taken as part of a Soil Conservation Service survey in 1938.

“My jaw dropped,” Mountford recalled. “These photos showed SAV that was 1,000 feet offshore in the Patuxent River. Nothing I had ever seen prepared me for that.”

Although the date on the photo was April 24 — still early in the growing season — the photos showed grasses growing in areas where the water would have been over a person’s head.

Mountford, now an independent estuarine ecologist and environmental historian who writes for the Bay Journal, pushed for a review of other old photos to determine the past extent of grass beds.

He found little interest until Naylor picked up the idea and tracked down other historical photos for the Patuxent.

Using photographs from 1952, Naylor estimated that the mesohaline (moderate salinity) portion of the river had about 1,729 acres of grass beds. Today, the Patuxent has only about 100 acres of grass beds, and almost all of that is in the freshwater portion of the river. “It’s not a little change,” he noted. “It’s a massive change.”

Naylor also examined 1938 photos, but those pictures did not cover the entire river. In areas where he could make comparisons, though, Naylor found almost twice as much grass in 1938 than was present just 14 years later.

In Virginia, scientists at VIMS have found much the same story in the James River. Surveys in recent years have consistently found less than 200 acres of grasses in the entire river.

But when VIMS scientists began reviewing aerial photos taken during the 1930s and 1950s, they identified 4,063 acres of grass beds in the river. Ken Moore, the VIMS scientist overseeing the historical review of grass beds in Virginia, called those figures “a conservative estimate.”

That’s because the pictures being used were taken for other purposes — usually surveys made by the U.S. Department of Agriculture’s Soil Conservation Service to determine land use and the types of crops being grown. “Obviously, since they weren’t taken for these purposes, they are not the best,” he said.

Today, flights made for SAV surveys follow rigorous procedures, flying during low tides on clear days, and early in the morning to avoid glare on the water surface. The older photos were often taken at midday, and sometimes during high tides. As a result, grass beds are sometimes obscured. “If SAV doesn’t show up, it could be because of those constraints,” Moore said. Still, he added, “many of these photographs are good for SAV purposes.”

And what the pictures reveal is striking. The Potomac was once so clear that 63 percent of the grasses in the tidal freshwater areas grew in water more than 2 meters deep.

Off the mouth of the Susquehanna flats, where only sparse grass beds grow today, the photos show SAV extending far offshore along a vast stretch of shoreline. “In Susquehanna flats,” Naylor said, “you are talking about miles of SAV.”

In a single grass bed off Smith Island, Naylor counted about 11,000 acres of grasses. That’s equivalent to one-sixth of what is in the entire Chesapeake Bay today.

In some places, the grass beds of the past are so vast they can’t be measured because they extend beyond the edge of the photograph. In those cases, only those beds that are positively seen can be counted.

The photos are like looking back in time. They show rich SAV beds where Reagan National Airport, built in a filled portion of the Potomac River, stands today. Some images show dikes being built in the middle of vast grass beds to make way for the airport.

Photos from the 1950s show shell craters in grass beds around a ship once used for Navy target practice off Bloodsworth Island. Few grass beds are in the area today.

In another photo, a tiny clamming boat can be seen in a vast ocean of grasses in Tangier Sound, an area critical to juvenile blue crabs that has suffered massive losses.

Work has only recently begun to find lost beds in Virginia tributaries beyond the James, but already, Moore said, dramatic changes have been observed. “It’s amazing,” he said, “there is so much in the Rappahannock” — a river with relatively few grass beds today.

In recent decades, Moore said, the biggest declines have been in low-salinity areas — often near population centers — and are likely related to water quality impacts from development. In the James River, for instance, a series of reconstructed historical photos show a steady decline in grass beds over time as one moves downriver from Richmond.

In addition, the grasses tended to decline first in deep water areas as sediment and algae increased, blocking light to the plants.

The photos should allow for better restoration goals than the Bay Program has had in the past.

Right now, the Bay Program has three goals: the first calls for restoring 114,000 acres of grass beds. That’s roughly the amount of area where grasses have been observed at some point since the early 1970s, although that much has never been observed at one time.

Longer term objectives called for restoring grasses to a depth of 1-meter, and ultimately to a 2-meter depth — roughly 600,000 acres.

But grasses aren’t likely to grow in all of those areas. Currents, the condition of the river bottom and other factors would prohibit the growth of grass beds. The photos show where grasses actually grew. “This will be a more realistic goal to shoot for,” Moore said.

At the same time, the figure that emerges will be far greater than the 114,000-acre goal. In the James, that would have meant a target of just 264 acres — only a bit more than is present today, but far less than the more than 4,000 acres present only a few decades earlier.

The photographic evidence of past grass beds is also expected to provide one of the strongest, most tangible arguments in favor of new water quality criteria.

When a tributary strategy was being developed to set nutrient and sediment reductions for the James a few years ago, some people were reluctant to adopt strict goals based on SAV needs — no one had ever seen extensive grass beds. Their minds were changed when the VIMS data became available.

“Not until they saw that historical evidence were people convinced that we should be pushing for the restoration of grasses as a goal for the James,” Batiuk said.

Naylor said he expects the new Bay and river SAV goals will be nowhere near the 600,000-acre estimate. One reason is the photographs show that grass bed locations tend to shift over time. When there are photographs of the same area from different years, the mapping project uses the image with the largest grass bed.

In some cases, that means that areas with grass beds in other years are not mapped. As a result, he said, it’s possible there were 600,000 acres of grass beds in the Bay, but not at one time.

Whatever target emerges, he and others say the lost grass beds of the Chesapeake won’t come back just as the result of better water clarity. Many areas have had no grasses present for decades, so there is no reservoir of seeds or plants to start a recovery.

The photos should help with that, too, by helping to prioritize areas for restoration efforts such as grass plantings. “We want to focus on sites where SAV used to grow,” Moore said. In that case, the photographs of the past may, indeed, be providing a picture of the future.