It was a champagne day on the James River: blue sky, puffy white clouds, sun sparkling on fast-moving water. With Jamestown slipping behind us, we headed downstream in the wake of Capt. John Smith, the first Englishman to explore the broad waters and many rivers of the Chesapeake Bay.

Captain Smith—no relative, I'm sad to say—was among that original band of dreamers and schemers who came ashore on the banks of the James 400 years ago, in May 1607. The settlement they established at Jamestown gave the English their first enduring toehold in the New World and wrote the opening chapter of our national narrative. The 400th anniversary of that event will be celebrated May 11 to 13 as America's Anniversary Weekend, and with an expected visit this month by Queen Elizabeth II of England.

But once Jamestown had survived its first winter and was more or less stabilized, Smith, then 28, set out again, on June 2, 1608, with a crew of 14 men. They were entering the continent's largest estuary—some 195 miles long, about 35 miles at its widest, 174 feet at its deepest, draining a watershed of about 64,000 square miles spread over what is now six states. The bay's shoreline is an astonishing 11,000 miles long because of all the nooks and crannies created by the 19 major rivers and 400 creeks and tributaries that flow into it.

Smith knew none of this, of course; he was leaping into uncharted waters.

He had a mission. He and the other colonists were under instructions from their sponsors, the Virginia Company of London, to find gold and silver, as the Spanish had done in Mexico and Central America. More important, they were to find the fabled Northwest Passage, a navigable route across the American continent that 17th-century Europeans fervently believed would provide a shorter path to the riches of the Orient.

In three months of extraordinary exploration, Smith covered some 1,700 miles; met, traded and fought with Native tribes; put down a near mutiny; ordered his own grave dug; compiled a detailed journal; and drew a map of the bay so accurate that it guided settlement of the area for the next 50 or more years. To commemorate Smith's achievements, Congress last December established the Captain John Smith Chesapeake National Historic Trail, the first such pathway on water.

Through his travels, Smith discovered that while the Chesapeake might not contain gold or silver, its wealth could be measured in other ways. Over the next three centuries, its legendary stocks of oysters, blue crabs and rockfish would feed and delight a growing nation; as late as the mid-20th century, the bard of Baltimore, H. L. Mencken, celebrated the bay as "an immense protein factory."

Last summer and fall, I re-created major segments of Smith's voyages, traveling in a 48-foot trawler, my own 40-foot sailboat or, in shallow waters, a 17-foot Boston whaler piloted by John Page Williams, the senior naturalist for the Chesapeake Bay Foundation. My notion was to contrast the wild and magnificent bay that John Smith discovered with the less wild, but frequently magnificent bay of today.

Few people know the bay as well as Williams, who has explored it as boy and man for more than 50 years. "If you compare it to John Smith's day, it is very much a compromised ecosystem," he says. "For four centuries, we have forced the bay to adapt to us and our lifestyle, with predictable consequences."

Of course, when Smith arrived, there were only 50,000 to 100,000 people—all of them Native Americans—living along the bay's shores. Today, the population of the watershed is more than 16 million, and according to the U.S. Census Bureau, 170,000 new residents move in every year. Four hundred years ago, there were 1.6 people per square mile; today, there are 250, a 15,000 percent increase.

Most of the bay's current problems stem from that growth. Its waters are clouded with storm runoff, sediment and waste; its stocks of fish and shellfish have been depleted. Last year, scientists declared some 35 percent of the bay proper a "dead zone," with too little oxygen to support life.

In retracing much of Smith's route, I was not surprised to find places where the hand of man lay heavy on the landscape and the industrial roar never stopped. But I also found extraordinarily beautiful places that look today much as they must have when he first saw them.

Heading down the James with the current behind us, Solveig III, the elegant trawler owned by my friends John and Barbara Holum, was making good time. Refugees from the Democratic political wars, the Holums now live aboard their boat. As for me, I have sailed and lived on the Chesapeake for 30 years and must confess that, for all its problems, I am as besotted with it today as when I first saw it.

Standing on the foredeck, I could not imagine what John Smith would have made of the view. Mansions now stand along the James' hilly northern bank, and a ghostly fleet of mothballed Navy ships is moored mid-river. Huge aircraft carriers dock at the Norfolk Naval Base. Giant cranes loom like pterodactyls over the humming shipyards of Newport News.

In his day, Smith saw "a very goodly Bay...that may have the prerogative over the most pleasant places of Europe, Asia, Africa or America for large and pleasant navigable rivers," he wrote in A Map of Virginia, published in London in 1612. "Heaven and earth have never agreed better to frame a place for man's habitation."

Leaving the James, as Smith did, we crossed the bay's 18-mile-wide mouth to Virginia's lower Eastern Shore. With the Atlantic just to the east, the waves and breeze picked up sharply and we could smell the ocean. We were traveling in significantly greater comfort than Captain Jack, as we took to calling him.

He and his men explored in an ungainly 30-foot boat called a shallop. It had been built in England and shipped across the Atlantic in two sections in the hold of a larger ship. It was strong and heavy (a replica built for the 400th anniversary celebration weighs 5,000 pounds), powered by ten-foot oars or two sails, and steered by a big wooden rudder—in short, a clunker of the first order.

At 30 feet long and about 8 feet wide and entirely open to the weather, the shallop provided close quarters for 15 men who frequently slept aboard, lest they be attacked ashore. What's more, the captain and his quarrelsome crew often wore English woolens and armor as they rowed and sailed under the broiling Chesapeake sun. Many Englishmen of the time bathed once a year or so, believing it to be unhealthy. I suspect the Natives, who bathed daily, could smell them coming.

Captain Jack's first stop, and ours, was Cape Charles, where, he noted, "The first people we saw were two grim and stout savages...with long poles like javelins headed with bone. They boldly demanded what we were and what we would." The pair were apparently friendly Accomack Indians, and from them Smith learned that the cape was the tip of a peninsula, not the mainland, so he headed north up the bay in pursuit of his goals. As did we.

And just like Smith, we encountered a line of strong storms, with 30-knot winds and four- to five-foot seas. Solveig III handled the weather easily, but Captain Jack and his crew nearly foundered.

"The wind and waters so much increased with thunder, lightning and rain that our foremast and sail blew overboard," he wrote. "Such mighty waves over-racked us in that small barge, with great labor we kept her from sinking." In other words, they bailed like crazy, probably with their hats.

"Two days we were forced to inhabit these uninhabited Isles, which for the extremity of gusts, thunder, rain, storms and ill weather we called ‘Limbo,'" he wrote. But then the storms passed. The crew's tailor cut up their shirts to mend the boat's torn sails, and they resumed their journey, heading up the nearest large river.

Following John Smith's route, we had a smooth run up the meandering Nanticoke River, admiring the eagles gliding above and the rich marshes on either side. But again, it was not so for Smith and his crew. They were met by a hail of arrows from the Nanticoke Indians. "The people ran as amazed in troops from place to place and [some] got into the tops of trees," Smith wrote. "They were not sparing of their arrows nor the greatest passion they could express of their anger."

Smith and company anchored in mid-river, out of arrow range, for the night. The next day, the Nanticoke "came unarmed," Smith noted, and started "dancing in a ring to draw us on shore." But the Englishmen, "seeing there was nothing in them but villainy," scattered them with musket fire.

After this first hostile encounter, the Nanticoke eventually made peace with the strangers and welcomed them by trading fresh water and food for trinkets.

Today, Sewell Fitzhugh is not sure that was such a good idea. "We should have burned the boat and killed them all," he says, mildly.

Fitzhugh is chief of the Nause-Waiwash tribe, which combines the remnants of the Nanticoke and three other tribes that are still struggling for official recognition as Native Americans from the state of Maryland. The tribe will help celebrate Jamestown's 400th anniversary and Smith's voyages this year and next, but Fitzhugh says it will do so only to make a point: "John Smith did not bring civilization here. There was already civilization here."

The Nanticoke story is all too painfully familiar. When John Smith arrived, the Nanticoke could put 5,000 warriors in the field; today there are a mere 300 registered tribal members in the area. As English settlers moved in, they pushed the Natives downriver into the marshes and all but wiped them out. "This land was our land; it was taken from us illegally," Fitzhugh tells me after we dock in Vienna, Maryland, 20 miles up the Nanticoke. "We are Maryland's forgotten people, and we are becoming strangers in our own land."

At Vienna, a pretty little town of 300 souls, we were joined by John Page Williams, who carried his whaler on a trailer and introduced us to the mayor, Russ Brinsfield, another passionate advocate for the bay who is also a farmer and an agronomist at the University of Maryland.

In a patchy drizzle, we motored up the Nanticoke and across the Delaware state line to Broad Creek, which is marked on Smith's map as the apogee of his Nanticoke exploration. It's one of many sites where his journal says he planted a brass cross to claim the land for King James. But not one of the crosses has ever been found, or at least acknowledged. Historians suspect that the Indians promptly melted them down and put the metal to other uses.

Brinsfield is campaigning for a single idea—that farmers and environmentalists need not be at cross-purposes. Agricultural runoff contributes about 40 percent of the nitrogen and phosphorus that pollute the bay; he is working with farmers to limit that runoff by planting winter cover crops and creating buffer strips between their fields and the water. Tests show that the river's water quality is improving as a result, but he remains skeptical about the bay's future.

"I worry about the marginal progress we are making in agriculture being offset by the pressure of human development," he says. "Frankly, we'll be lucky to maintain the status quo against development for the next 20 years." Vienna is already feeling the pressure: its master plan assumes that the current population will triple over the next decade.

Captain Jack did not stay long on the river. While feasting with the now-friendly Nanticoke, he heard that tribes on the bay's Western Shore could describe the territory to the west and any Northwest Passage out of the bay. Soon, Smith set off down the Nanticoke and across the bay. We did the same, crossing through what is today Hooper Strait.

"So broad is the Bay here," Smith wrote, "we could scarce perceive the great high cliffs on the other side." Suddenly, as the morning mist cleared, we experienced one of those electric moments when his journal came alive. What he saw, we saw: the Calvert Cliffs, just north of the mouth of the Patuxent River, gleaming on the horizon.

They dominate the landscape, and from a distance, they must have looked promising to Smith. This, surely, was the route to gold and silver and the Orient.

It was nothing of the sort, of course, as Smith would learn. But for us, there was another reward: the insight of scientists at the Chesapeake Biological Laboratory. It is an arm of the University of Maryland's Center for Environmental Science, a leading research institution on the bay. At the CBL campus on Solomon's Island, I ask Walter Boynton, a senior scientist who has studied the bay for three decades, what Captain Jack would have seen beneath his shallop as he explored the Chesapeake.

"Really clear water," Boynton says. "He could see the bottom at 30 feet. Today, we can only see a few feet down. Smith would have found scores of different kinds of fish, oysters and clams, maybe 13 or 14 species of sea grass. The rivers would have been deeper, able to take transatlantic shipping up to the fall line."

Ed Houde, a fishery expert at CBL, says Smith would have encountered "huge amounts of oysters—100 times or more than what we have today, and more rockfish and larger fish. Remember, as late as the 1890s, watermen were harvesting at least 15 million bushels of oysters a year, compared with maybe 100,000 today....There could have been billions of oysters on the bottom. The reefs were so tall that they could break the surface at low tide."

Despite the bay's natural bounty, Smith's crew was wearing out as the men continued their journey up the bay's Western Shore. Barely two weeks out of Jamestown, they had survived repeated thunderstorms, fought off assaults from Indians and seen their fresh water run low. Nearly mutinous, they now begged Smith to return to Jamestown.

Instead, he delivered a pep talk: "As for your fears that I will lose myself in these unknown large waters, or be swallowed up in some stormy gust," he told his men, "abandon these childish fears, for worse than is passed is not likely to happen and there is as much danger to return as to proceed."

Brave talk, but after another storm, and with some of his men too weak to go on, Smith agreed to turn back on June 16. They sailed south to the mouth of the Potomac, but by then they had "regained their...old spirits," as their captain had exhorted them to do, so they turned up that river. Some 60 miles later they reached the Indian settlement of Patawomeck, where the chief provided guides to lead them to a mine at the head of today's Aquia Creek. Here, they had heard from the Patawomeck, the Indians scraped a silvery dust from the rocks.

On a sunny September morning, Williams and I skimmed up the creek in his whaler, past beautiful houses, under an Amtrak bridge and, slowing to observe the six-mile-per-hour speed limit, past the little community of Aquia Harbor to a point where the creek trails off in a field of yellow waterlily pads, some 11 miles up from the Potomac. It was beautiful, but hardly as Smith experienced it. Route 1 traffic roared to the west, a helicopter thudded overhead en route to the Quantico Marine Corps Base and an airliner descended on Reagan National Airport across the river from Washington, D.C.

Smith and his guides marched farther west, toward the Piedmont, and found the mine, but again Smith was disappointed. What the Indians extracted was probably antimony—silvery, to be sure, but not silver. It was a powder they used to dust their bodies during ceremonies. Smith gathered several bags full and had it assayed later, but noted that "all we got proved of no value." Once more, the Virginia Company shareholders back in London would come up empty-handed.

But it was dawning on Smith that if the Chesapeake might not proffer precious metals, it was still stunningly rich. Its shores abounded with timber that deforested England needed desperately to build houses and ships; its wildlife inspired visions of limitless supplies of fur and food. "Neither better fish, nor more plenty, nor more variety for small fish had any of us seen in any place," he wrote. (Lacking nets, he and his crew tried catching them with a skillet, to little avail.)

Smith did not even consider the crop that would ultimately enrich the early settlers of the Chesapeake: tobacco. The gentry in London were just getting hooked on the stuff they were importing from Spanish colonies.

Heading south again toward Jamestown, Smith's boat ran aground off the mouth of the Rappahannock River, at present-day Deltaville, Virginia. While waiting for the tide to turn, Captain Jack used his sword to spear a stingray—which promptly stung him on the arm. It was here that Smith, in torment and with one side of his body swollen, told his men to prepare his grave. From this episode, the tip of Deltaville received the name it still bears, Stingray Point.

Today, it's a cluster of cottages around a small beach at the tip of a peninsula. Strolling on the sand last June, I met a plus-size woman in a bikini smoking a cigarette next to a cooler of beer. When I asked if she thought this was the spot where Capt. John Smith ran aground in 1608, she took a drag and said, "Honey, I really couldn't say. I wasn't here at the time."

Deltaville is a funky little town (unofficial motto: "We're here because we're not all there") and home of the Deltaville Maritime Museum, a small jewel devoted to the place's rich boat-building history. Volunteers built their own replica of Smith's shallop here last year, and it will participate with two others in Jamestown anniversary commemorative ceremonies in July.

"John Smith's landing here was probably the most famous event in Deltaville's history," Raynell Smith, the museum president, said with a smile. "He was our first unhappy tourist."

But Captain Jack's misery did not last long. The physician in his crew applied an oil to the wound, and by evening, the crew's journal notes, the captain's "tormenting pain was so well assuaged" that he ate the stingray for dinner.

By July 21, Smith's boat was back in the relative comfort of Jamestown, being restocked. Three days later, on July 24, Smith and a dozen men, eight of them veterans of the first voyage, set off on a second. This time, they sailed all the way to the head of the bay, near present-day Havre de Grace, Maryland, in pursuit of the Northwest Passage.

Solveig III did the same on a hazy, humid July day. In those conditions, it was easy to understand why the explorers first believed that the bay divided into "two heads," or rivers, referring to the Susquehanna on the west and the Sassafras on the east. It's only when you get closer that you can see the tall cliffs of Turkey Point and the Elk and Northeast rivers opening between the other two.

The huge Susquehanna flows south through New York and Pennsylvania and provides 50 percent of the fresh water that flows into the bay above the Potomac. But Smith noted: "...we could not get two days up it with our boat for rocks."

Those rocks, known today as Smith's Falls, made it instantly clear that navigation to the west was impossible. The Susquehannock Indians confirmed this to Smith and his men. The Indians did say there was a "great water beyond the mountains," probably referring to what is now the Ohio River or perhaps Lake Erie, but the crew took this to be "some great lake or river of Canada," not the Pacific or a route to the Orient.

This is where the dream of the Northwest Passage ended, as far as John Smith and the Chesapeake were concerned. No doubt he was disappointed, as his backers in London would be, but he would still leave his imprint on the bay's shores.

The map of the Chesapeake that Smith published in 1612 was the first to get into general circulation in London. It became the document that Stuart kings used to distribute land grants over the subsequent decades. The next generation of colonialists used it to lay out their future settlements. In essence, John Smith was the cartographer of the new nation.

Captain Jack's excellent adventure was coming to a close. On his way down the bay, he explored two major rivers on the Western Shore, the Patuxent and the Rappahannock. And in the middle reaches of the Rappahannock, he got a lesson in Native military tactics.

As Smith navigated a narrow portion where the river turns to the left, a band of Rappahannock Indians let fly with a volley of arrows from the wooded cliffs on the right. Smith steered quickly to port toward a low marsh—until more Rappahannock sprang up from the reeds and shot at the boat from that side. The Englishmen pinned the Indians down with musket fire and continued upriver, but, Smith noted, "when we were near half a mile from them, they showed themselves dancing and singing very merrily." The Rappahannock, it seems, were not above a little taunting.

Williams and I retraced this route in his whaler with Edward Wright Haile, a leading authority on Jamestown and Colonial American history who lives on a small creek off the Rappahannock. Williams beached the boat on the starboard shore, and Haile and I climbed the cliffs to where he believes the Rappahannock fired their first volley. At 150 feet, atop the cliffs but hidden in the woods, they had a terrific angle of attack. The river was at our feet, the marsh just beyond, and the view to the west was unbroken for 30 or 40 miles.

"They were obviously very good military strategists, even if their weapons had limits," Haile said. Then, gesturing out over the river and marsh toward the Piedmont to the west, he added: "All of this looks today largely as it did then."

Back in the whaler, we continued upriver toward Fredericksburg, Virginia. It was drop-dead gorgeous on this September day. More than a dozen bald eagles soared above the steep, forested right bank, ospreys dived for fish in the river and great blue herons and egrets stepped delicately among the wild rice and other grasses in the marsh.

The river looked lovely, but that is what is so deceptive about the Chesapeake watershed generally: its very beauty masks its ecological problems.

In John Smith's day, this river would have been clear and filled with rockfish, sturgeon, American shad and herring. Today, only the rockfish and a few other species abound in its cloudy waters, and they are thriving largely because of severe limits imposed on fishing in the latter 1980s.

Bay-wide, the statistics on key environmental factors in the Chesapeake are discouraging. For example, the Chesapeake Bay Foundation estimates that in 1607 there were about 400,000 acres of underwater grasses in the bay. Today, there are only about 70,000. Wetlands, which the foundation calls the bay's "lungs and kidneys," amounted to 3.5 million acres. About 1.5 million acres remain. Virtually the entire watershed was forested in 1607, constituting a "great, green filter" for the natural runoff into the bay. Much of that has been cleared for agriculture and development. And the oyster population, which once could filter all the water in the bay every few days, is less than 4 percent of its historic high.

Each year, the foundation produces a State of the Bay report, which measures 13 key indicators of the Chesapeake's health, from pollution to fisheries to crabs. Using the bay in John Smith's time as an index of 100, the foundation rated the bay last year at 29, up two points from the year before, but still perilously low.

That's a failing grade, given the pledges of federal, state and District of Columbia governments over the past two decades to spend the billions necessary to clean up the bay. In 2000, the leaders of those governments signed an agreement committing to restore the Chesapeake's health to a rating of 40 by 2010. Now, meeting that goal seems unlikely.

The problem is not a lack of knowledge of what needs to be done. "The bay is one of the most studied, analyzed, examined bodies of water on earth," says the Chesapeake Biological Laboratory's Boynton. "We scientists are doing a great job chronicling the demise of the bay. What is lacking is the political will to halt that demise."

On the bay's western shore, at the head of the Rhode River, Anson (Tuck) Hines, director of the Smithsonian Environmental Research Center, has tracked the changes for 30 years. "We are at the tipping point," he says. "Global climate change, the pace of development, the decline of the fisheries—everything is happening so quickly that I worry about the next 40 years, much less the next 400."

A shared sense of alarm about the bay is what motivated John Page Williams, the Conservation Fund, the National Geographic Society, the Chesapeake Bay Foundation and others to push Congress to authorize the Captain John Smith Chesapeake National Historic Trail.

The trail recognizes Smith's route as an important chapter in America's early history, just as the Lewis and Clark National Historic Trail, the Oregon Trail and 14 others mark other pioneering achievements. Once fully laid out by the National Park Service, both land sites and interpretive buoys will offer historical and scientific information at key points along Smith's circuit. Boaters and others will be able to trace his voyages and access information via cellphone and the Internet to contrast the bay now with what was known about it in his time.

"We think it will build a constituency for the bay," Williams says. "The trail will explain to people what...the possibilities are if we are able to restore it to something close to what it once was."

A tall order, perhaps. But if the water trail succeeds, it will constitute only Capt. John Smith's latest contribution to the splendid Chesapeake.

Terence Smith was the media correspondent and senior producer for "The NewsHour with Jim Lehrer." Photographer Richard Olsenius is based in Annapolis, Maryland.