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After living along the Laguna de Santa Rosa for decades, Joe Aggio and his family have grown accustomed to having their land swamped with water, as has been the case this year, the waterway swollen to its greatest extent in more than a decade.

But the floodplain around their dairy farm also has become much more of a nuisance over the years.

Aggio, 32, said the wetland around his farm between Occidental Road and Guerneville Road used to be manageable and clean, flooding in the winter before draining off so his family could grow crops to feed their cows. But the waterway has become increasingly plugged with sediment, invasive Ludwigia plants, garbage and other discarded items like shopping carts and couches, he said.

“It no longer flows. It no longer drains. It’s just a stagnant mess,” Aggio said. “We’ve lost crops because of it. We haven’t gotten crops in because of it … It’s become increasingly difficult to farm the land.”

So Aggio’s hopes were raised recently when Sonoma County Water Agency officials secured a grant to move forward with plans that could eventually help alleviate the challenges faced by his farm and other landowners along the 22-mile waterway.

With funds from the California Department of Fish and Wildlife, the Water Agency and environmental groups are embarking on a massive planning effort to revitalize the watershed that stretches from Cotati north to Windsor and takes in rural areas east and west of Santa Rosa.

The watershed, which includes Mark West and Santa Rosa creeks and many other smaller streams and wetlands, has been altered significantly over generations by agricultural and urban development.

One result of its transformation is the Laguna now fills with more sediment than it once did, at times hampering its ability to drain floodwaters into the Russian River.

“If this happens over a very long period of time — we’re talking hundreds of years — that eventually will get to a point where it could back up drainage back into Santa Rosa, Cotati and Rohnert Park,” said Mike Thompson, assistant general manager of the county Water Agency. “This is well beyond our lifetimes, but if it keeps filling up like that, the storage and flood protection of the Laguna that naturally occurs is being taken away.”

Armed with $517,000 in state grant funds, the Water Agency and other groups expect to spend the next three years developing a comprehensive restoration plan for the watershed. Project partners include the San Francisco Estuary Institute and the Laguna de Santa Rosa Foundation.

The Water Agency is leading the planning effort, while the Laguna foundation’s work includes helping with conceptual design and prioritizing possible restoration projects. The estuary institute’s work includes drafting and finalizing the restoration plan itself, as well as facilitating conversations with experts on conceptual designs.

“There’s a lot of groups working on doing restoration or working on improving water quality in the Laguna-Mark West watershed, but we’ve gotten to a point where some of the problems are so big, they can’t really be tackled alone, and we need sort of an overarching plan in order to move forward,” said Wendy Trowbridge, director of restoration and conservation science programs at the Laguna foundation.

Historically, sediment in the watershed used to pile up at the base of mountains in the Santa Rosa Plain, but man-made channels now act “just like firehoses,” delivering sediment straight into the Laguna, Trowbridge said.

Sonoma County Supervisor James Gore compared the watershed to a bathtub, and the Laguna itself to a drain that needs to be cleared.

“If your drain is clogged, you can never have a healthy system. That’s why it’s so important,” Gore said. “This grant allows us to focus our efforts on how to fix that drain.”

The Laguna is also challenged because it has accumulated nutrients — namely nitrogen and phosphorous, byproducts of fertilized agriculture — that have allowed invasive plants and algae to grow, which can render the waters uninhabitable to other life, Thompson said. Restoration work could work to reduce the nutrient load that enters the watershed as well as cleaning up what’s already there, Thompson said.

Gore said a key component of the restoration will be to ensure any changes are not just one-time fixes.

“The idea is not to do a cleanup every year but to restore some of the lost natural processes ... so that the system works better,” Gore said. “That’s the goal of the Laguna — to restore the process so that it’s a well-functioning drain.”

Trowbridge suggested the restoration could also look at potential spots where the watershed’s historic marshes, which helped clean out nutrients, could be restored.

The planning process will build on work already done by the estuary institute, which recently completed a project examining the historical extent of the Laguna and comparing it to the landscape now, according to lead geomorphologist Scott Dusterhoff. The institute will expand the footprint of its historical ecology mapping to better understand how the ecosystem used to function and help develop a vision for the future, Dusterhoff said.

The planning process is expected to be a large undertaking, involving public outreach, stakeholder meetings and extensive amounts of historical research. Dusterhoff said it will take extensive work.

“It’s not just going online and searching digital archives. It’s going to historical societies. It’s going in people’s basements whose great grandfather collected a lot of historical photos,” Dusterhoff said.

“It is a very labor-intensive endeavor.”

Thompson characterized it as a passion project for the Water Agency, where there was “a lot of whooping and hollering” when staff members found out they would receive the grant, he said.

The agency has the legal right to undertake the project but is not obligated to do so, according to Thompson.

“There’s a lot of projects we have to do, and then there are some projects that are just good for the soul. I think it’s important for an organization to do these kinds of projects that make the world better,” he said. “This is one of those.”

You can reach Staff Writer J.D. Morris at 707-521-5337. or jd.morris@pressdemocrat.com. On Twitter @thejdmorris.