Representatives from federal, state and private-sector agencies gathered in La Crosse Monday to celebrate three decades of efforts to balance commercial and ecological interests on the nation’s largest drainage system.

Established by Congress in 1986, the Upper Mississippi River Restoration program was the nation’s first large-scale environmental project combining habitat restoration and ecological monitoring, bringing together organizations including Corps of Engineers, the U.S. Fish and Wildlife Service, the Environmental Protection Agency and natural resource department from four bordering states.

In its three decades, the river program has funded 55 projects that have restored more than 100,000 acres of habitat between St. Paul, Minn., and St. Louis, including the construction of dozens of islands near La Crosse designed to protect aquatic vegetation and reduce sedimentation.

John Anfinson is a river historian and superintendent of the Mississippi National River and Recreation Area, a 72-mile national park that follows the river from the Twin Cities to Hastings, Minn. In his book “The River We Have Wrought,” Anfinson describes four distinct Mississippi Rivers, starting with the natural waterway that flowed for thousands of years before the arrival of European settlers.

A maze of sandbars, islands and flood plains, it had no continuous channel and had an average depth of less than two feet north of Prairie du Chien.

“It’s not folklore that people once waded across the Mississippi River,” Anfinson said.

By the early 20th century, the Corps of Engineers had constricted the river with wing dams and other structures, improving navigation but compromising the backwaters that fish need to survive the winters. In the 1930s, the Corps constructed the lock and dam system, flooding islands and further silting in backwaters.

This is what Anfinson calls the “third river.”

By the 1960s, scientists and environmentalists began to raise concerns over the changing riverscape and the dwindling fish populations. After decades of fighting between commercial and environmental interests, Congress adopted a plan to restore habitat and establish long-term monitoring stations to measure its progress.

“Our goal was to put environmental resources on the same par as barge traffic and navigation,” said Dave Kennedy, then a Department of Natural Resources biologist who worked with former U.S. Rep. Steve Gunderson to craft the bill.

Conservation groups like the La Crosse County Conservation Alliance distributed postcards up and down the river for citizens to contact key lawmakers.

“That made a difference, because it was grass roots,” said Marc Schultz, the group’s chairman. “River rats are everywhere.”

It has led to what Anfinson calls the “fourth river,” one where human intervention seeks to balance commerce with the natural landscape.

“We can’t just let that third river happen,” he said. “We are actually trying to change the river.”

The results are apparent, said Jeff Janvrin, a Mississippi River Habitat specialist with the Wisconsin DNR.

In the early 1990s, DNR biologists were finding essentially no game fish in Pool 8, Janvrin said. Within seven years of the project, surveys were turning up 400 to 500 blue gills and 100 bass per hour.

The program has also helped wildlife managers develop techniques that can be applied in other places, such as West Salem’s Lake Neshonoc.

“The river program is just phenomenal when you think about the technology that has been developed,” Schultz said.

Just as important as the habitat restoration was the monitoring network, which created what Mike Griffin, the Iowa DNR’s Mississippi River wildlife biologist, calls “the best long-term data set in the world.”

“We’re at a much different place than we were 20 years ago or 30 years ago because we have so much information,” said Kirsten Mickelsen, Ecosystem and Navigation Program Director for the Upper Mississippi River Basin Association.

Despite the program’s successes, there are ongoing challenges.

Mickelsen said sedimentation — the result of urban and agricultural land uses that push water off the land — remains the single biggest threat to the river system.

Even 30 years in, Anfinson said the restoration program is still just a test. After all, the first river took thousands of years to reach equilibrium.

“Is the river’s ecosystem sustainable … or are we just putting patchworks on?” he said.

Either way, he said, “We will tend this river as a garden, indefinitely.”