When I stand on top of a rock overlooking the Harlem Meer with Eric W. Sanderson, after seeing his exhibition, “Mannahatta/Manhattan: A Natural History of New York City” at the Museum of the City of New York, I begin to see the city the way the show suggests, the way Mr. Sanderson has come to view it after nearly a decade of historical exploration and computer simulation.

Mr. Sanderson, a landscape ecologist for the Wildlife Conservation Society at the Bronx Zoo, looks past the man-made lake below us, at the northeastern corner of Central Park, and points to where a stream once stretched, leading along 125th Street toward where we now stand.

To the north, he explains, the forested growth of 400 years ago would have begun to thin out into lands that the Lenape Indians might have farmed. And leading toward the East River a wide tidal inlet would have flowed, setting the wide dimensions for East 106th Street. Ten minutes later, as we approach the Ravine in the park’s North Woods, Mr. Sanderson points to Montayne’s Rivulet, one of Manhattan’s original streams, now pouring over the rocks. Such streams were once so plentiful on this island, he explains, that their combined length was more than 66 miles.

Image Mannahatta/Manhattan: A Natural History of New York City includes an image combining a computer simulation of Manhattan in 1609 with a current photograph. Credit... Composite and simulation by Markely Boyer; photograph by Arthus-Bertrand/Corbis

But even without such an accomplished guide at your side, you emerge from this unusual exhibition looking at the local landscape in a very different way. Archaeologists typically discover ruins of human dwellings as they descend through layers of earth. Here, with the aid of historical accounts, archival maps, ecological principles and computer modeling, Mr. Sanderson has done almost the opposite, revealing not strata of the human past, but a natural world that preceded island records. Times Square was once the site of a beaver pond; Foley Square was the site of a freshwater pool that took care of most of Manhattan’s water needs for two centuries.