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Life in Santa Rosa and surrounding cities is made possible by a vast fortress, the product of more than a century of civil engineering projects that hold at bay the floods that nature is trying to send sweeping across the vast plain of central Sonoma County.

The Sonoma County Water Agency, the inheritor of that enormous but largely invisible system of streams and reservoirs, is now engaged in an epic engineering project of its own: trying to create a healthy, natural-looking ecosystem in the network without unleashing serious flooding in the cities.

"Basically the only purpose of these channels was flood control," said Assistant General Manager Mike Thompson, explaining a complicated map showing the miles of streams, ditches and ponds that wind around the urban core. "There was no consideration for water quality, no consideration for habitat."

The agency recently opened the fifth summer of what is likely to be a decade-long effort to convert the drainage channels to something that resembles natural, living streams. Assisted by hundreds of seasonal workers, including teams of at-risk youth known as the Sonoma County Youth Ecology Corps, agency employees are working through the painstaking job of trimming trees, removing sediment and invasive species and clearing mountains of brush and blackberry vines.

At the same time, the agency is trying to open up the ditches to use by the public, which had traditionally been kept out by fences or jungle-like undergrowth. The agency has opened some of its maintenance roads and allowed Sonoma County Regional Parks and other agencies to open trails along the flood control projects.

"We want the public to use these and appreciate these spaces," Thompson said, showing off a cleaning crew moving along a trail next to Santa Rosa Creek, one of the main flood control channels through the region.

The work is paid for largely with a portion of property taxes paid in Santa Rosa, Rohnert Park and Cotati designated for flood control maintenance, which brings in about $5 million per year.

The flood control system has been through several phases over 150 years of settlement.

In its natural state, the Santa Rosa area was a vast grassland that turned into a soggy wetland in the rainy season. Early settlers didn't find most of the streams and creeks as we know them today, but rather a series of shallow, grassy lakes fed by streams from the hills to the east, Thompson said.

Farmers in the 19th century created deeper channels through the region, establishing the framework of current creek beds. That dried out large blocks of land where the cities stand today.

"Without what they did, a lot of areas, Rohnert Park and Santa Rosa, could not have been developed," said Jon Niehaus, the agency stream maintenance coordinator.

But those newly defined streams still flooded occasionally, which became a problem as the post World War II development boom put houses on former farmland. Through the 1950s and '60s, engineers simply scoured out the creek beds to create highly efficient, but largely barren, gravel channels secured by fences, gates and concrete walls. They even buried a few streams in underground pipes; Santa Rosa's City Hall sits on top of a buried stretch of Santa Rosa Creek.

That changed again in the 1990s, when the effects of the urbanization began to tell on salmon, steelhead trout and other formerly abundant species. The addition of these species to state and federal protection lists left the Water Agency unable to use its traditional method of keeping the storm channels open: bulldozing out the sediment and plants every year.

For more than a decade, Niehaus said, the agency essentially quit doing stream maintenance on the system, allowing the formerly barren channels to become impenetrable tangles of trees, vines and grass. Not only did that impair the efficiency of the flood control project, but it allowed for the accumulation of trash and created hiding places for squatters and marijuana growers.

After years of study and consultation with state and federal regulators, the agency decided on a new approach: eco-engineering, or turning these channels into something that resembles a naturally occurring stream. Since 2008, crews have spent the summers in the labor-intensive work of clearing brush and training trees to create an open stream bed with a healthy leaf canopy overhead to shade the water, a better environment for fish, otters, and other creatures that formerly lived in the area.

Although artificially engineered, these streams are modeled on existing natural streams in other parts of the county and along the North Coast, Thompson said.

The result is what appears to be a natural stream, but is in fact a more ecologically friendly version of the flood control channels created by those engineers during the 20th century development boom.

Thompson doesn't fault his predecessors for their unsubtle approach to creating flood channels: Flooding was the problem they were asked to solve and they did so with great efficiency, a solution that still works well 50 years later.

"As time changed," he said, "people realized that these should be more than big drainage ditches."

And he is sure that his team's current engineering efforts will not be the last phase in the evolution of the area's huge flood control system.

"I hope that in 100 years," he said, "that they do find a way to do it better."