On a recent sunny day in the Napa Valley, Robin Grossinger cupped his hands around his eyes and surveyed the landscape. He said the scene gave him “a feeling of grandeur.”

He was not talking about the vistas of hillsides draped in vineyards, with their gnarled vines tinged green with new growth that by fall will be laden with the valley’s renowned cabernet sauvignon and other grapes. Mr. Grossinger, a scientist with the San Francisco Estuary Institute and author of the new Napa Valley Historical Ecology Atlas, had turned his gaze onto another charismatic species: a small line of valley oak trees.

While today’s visitors — around five million annually — come to drink wine and soak up the beauty of Napa’s viticultural landscape, past visitors came to marvel at the majestic oaks.

The area where Mr. Grossinger was standing, near Oak Knoll in the southern end of the valley, is where travelers entering from the south first took in the beauty of the oak savannas that defined the valley floor, bursting with wildflowers in the spring. The trees at Oak Knoll supported abundant wildlife and created shade in the heat, among other benefits, prompting the California State Senate in 1858 to declare them “at once an ornament and a blessing.”

While almost all of the valley oaks are gone from Napa — the savannas were largely cleared to make way for intensive agriculture in the late 19th century — a few pockets remain. The oldest trees, dating back more than 300 years, were alive when the Caymus, Napa, Canijolmano and Mayacma tribes managed the valley to produce abundant acorns, deer, salmon and other staples.

Unlocking the landscape in this way, so that the past is revealed in the present, is the almost magical outcome of Mr. Grossinger’s atlas (with design and cartography by Ruth Askevold), which was more than 10 years in the making. Working with a long list of collaborators, Mr. Grossinger unearthed maps, photos, surveys, old postcards and other information that added insight into how Napa has changed over time. “I spent more time in libraries than out in the field,” he said.

His detective work is characteristic of historical ecology, an environmental practice championed by Mr. Grossinger and the San Francisco Estuary Institute, which is gaining in popularity.

“It’s a little like solving a mystery,” said Shari Gardner, a researcher with Friends of the Napa River, who, as part of the project, scoured the area for valley oaks that had most likely been there at the time of European contact.

The atlas combines field research, scientific data, maps, historical photos, writing and records, creating a picture of the Napa Valley’s natural environment and how it has been shaped by human activity over time.

It covers the oak savannas, soil, creeks, wetlands, tidal marshlands and the Napa River, all features that make up the terroir, or unique characteristics of land and climate, that distinguish today’s best vintages. Wine is barely mentioned in the book, but one can practically taste it on every page.

The atlas also includes three suggested valley tours, with stops that include former tule grass wetlands and a good spot to see steelhead trout spawning.

Standing on a small bridge on the Napa River outside Yountville on a sunny day, an easy stone’s throw from some of the best wineries in the world, it was hard to perceive the environmental challenges facing the valley.

“Napa Valley has always been beautiful,” Mr. Grossinger said. “And it’s still beautiful.”

Then he explained how the Napa had changed over the years, from a meandering river with many side channels to the more controlled stream it is today, including problems with flooding, erosion and oversilting.

While currently productive, Napa, like many agricultural regions, is also fragile, vulnerable to climate change and to problems caused by poor watershed management, overuse of pesticides and other issues. Understanding the choices that created today’s landscape will help this generation make choices that will keep the area resilient for the future, he said.

Heading across the valley in midafternoon, Mr. Grossinger spotted a group of workers taking shade under one of the small fraction of remaining historical oaks. “Now that’s where you want to be,” he said.