Just moments after full dark, when the last shards of twilight slip away into the night, the junglelike woods outside my tent abruptly turn on, as if someone has thrown a switch. There are raspy screeches and deep, throaty grunts and the unsettling crack of branches being snapped in the underbrush. From the river nearby, something very large splashes and then exhales loudly. As I stretch out to rest, the hard-packed shell mound under me pushes through the thin tent fabric, outlining the knobby relief of thousands of freshwater snails gathered here by aboriginal campers centuries ago.

I am not...

Whales once breached here, somewhere above where I am now standing, thigh-deep in sawgrass at the river’s headwaters. They did so worldwide, of course, back when they were something other than whales and land was little more than the remnants of angry, fuming volcanic pinnacles. But age is the great divider, and geological time—or the lack of it—was, and still is, what has made Florida and its waterways unique.

A quarter billion years ago, when the Shenandoah Valley was becoming the mountainous gully that would carry the river of the same name, Florida was where marine animals still...

If Jackson Pollack were God, this is how he likely would have painted the upper St. Johns, a terrestrial canvas covered with tannic splatters and veins, elliptical cobwebs one step away from being random. Instead of following the sheet flow of this grassy river northward from the headwaters into the place where the map tells me the river should begin, we soar back to our put-in ramp at Blue Cypress Marsh, the speed of the airboat pressing the wind into my face.

If the Florida winter has browned out the marsh, it has also kept a check on the multitude...

The Econlockhatchee River quietly slips into the St. Johns just north of Puzzle Lake, snaking its way out into the prairielike marsh as if it were just one more lazy bayou sluicing back to the easterly edge of the palm and oak hammock shore.

The Econ, however, is far more ambitious than a bayou. Arising from its own swamp some 36 miles from the St. Johns, the creeklike river flows north and then east across the fringes of the Orlando metropolitan area, draining some 280 square miles of terrain and confluxing with the Little Econ on the way. To do...

Lake Monroe marks the very distinct place where—for most of the world—the St. Johns moves from the unknown and the unseen to the highly available. If the river upstream of here is a mystical Gregorian chant, then Monroe is Montavanni, as easy to find as an AM radio station.

A lone, stern-mounted paddlewheel steamship from the Hart Line spit and smoked its way to an extended wharf at Sanford here for the last time in 1929, ending an era of riverboat service to the town that first began in the 1850s. Today, the only working smokestacks to be...

The dark tea that is the river curls around the east side of Hontoon Island, beyond the clear creek of Blue Spring. As it does, it takes a bite out of the southwesterly shore of Lake Beresford before continuing its sullen seep northward.

Beresford appears before me as a great, shallow swath of water, gridlocked by woods, canopied thick like broccoli. There were once two busy steam-boat landings here, each with a wooden wharf and frame storage house at its end. An old photo from the 1890s shows the opulent paddlewheeler, the City of Jacksonville, moored at the end of...

Of the “notable mineral springs” Sidney Lanier once reported along the river in his guidebook, the three most powerful emerge from the hilly karst terrain of the Ocala National Forest. They seem spaced, territorially, along the western shore, each with its own hydrological fiefdom: Juniper to the south, Silver Glen in the middle, and Salt to the north. Geologically, all arise from the limestone and dolomite of the Ocala Uplift, sedimentary bits of sand and coral and shell laid down as sea bottom in the Eocene some forty million to fifty million years ago.

Juniper is a thin, enchanting scribble...

For a river as famous as the Ocklawaha, its confluence with the St. Johns is unheralded, accomplished through a subtle break in the cypress woods behind a vast pod of hyacinths and grassy maidencane on the western shore, little more than an aquatic murmur. Except for its presence on my map, there’s no indication that this is even the Ocklawaha at all: there are no signs, no markers, no classical Florida hype of the sort one might find on a terrestrial site of this magnitude.

Coming upon the Ocklawaha in this way is like walking into a deserted movie theater...

Palatka looms ahead now, and its arrival means I have seen the last of the narrow river and its elegant solitude. Between here and Jacksonville, the St. Johns becomes a broad aquatic boulevard, averaging two miles from one shore to the other—sometimes as narrow as a mile, other times splayed out between its high banks for three. It now seems more like a sensible northern river than a charming southern one.

Water managers call this the “main stem” of the river; Lanier called it “broad and garish”—but he did so in contrast to the more mysterious, gloomy Ocklawaha....

The massive Shands Bridge rises up from the water to the north, right beyond the easterly peninsula of Pacetti Point and Palmo Cove. After being lulled into a buzzlike complacency by the broad, repetitive nature of traveling through the middle of this lower river, the appearance of the bridge startles me, looming on the horizon like King Kong over the skyline of Tokyo, one long, low span engorged by a behemoth hump. The hump is the only way for any boat larger than a skiff to get under the bridge, and I aim for it.

I think of this bridge...

A palimpsest is an ancient manuscript that has been written upon and erased, over and over again, through the centuries. It uses a medium, like parchment, that is too rare, too valuable to discard. The St. Johns itself is surely one long and meandering palimpsest. And perhaps its most worked-over site is Jacksonville. There have been more people here, for longer times, erasing the past and re-creating the present, than anywhere else on the river—perhaps anywhere else in this entire palimpsest of Florida.

But like reinscribed parchment, the eras of the river will reveal themselves if held up to...