As commuters ready for construction delays at the Clinton ferry terminal, researchers are geared up to monitor innovative technology to mitigate the effects of terminal construction on the area’s underwater habitat.

Divers from the Battelle Marine Sciences Lab in Sequim recently transplanted 11,000 native eelgrass shoots in areas disturbed by the first phase of the ferry dock reconstruction in Clinton. To date, more than 14,000 square feet of eelgrass has been successfully transplanted, with more stockpiling planned as the reconstruction project enters its second phase. Eelgrass is part of salmon habitat in Puget Sound.

The planting is part of an environmental protection project that will cost the Washington State Ferries system more than $5 million in addition to what it is paying to rebuild the Clinton dock. But the money has paid for more than just plants.

“Restoration is not just about planting plants,” said Ron Thom, a Battelle scientist. “Restoration is a full-scale engineering project. If a bridge fails, we can determine the cause. If a habitat fails, we might never know why. That’s why we have to protect these areas.”

To protect salmon habitat and maintain a diverse underwater habitat off the Clinton shore, officials with the state Department of Transportation called in scientists and researchers from Battelle and the University of Washington to assess how and where ferry dock reconstruction would affect fragile ecosystems. The reconstruction was inevitable due to increased traffic on the aging, wooden dock, so scientists sought ways to avoid destroying the eelgrass beds beneath and around the Clinton dock.

The most obvious need for eelgrass beds was sunlight, so allowing as much light through the dock became an engineering priority. Other concerns stemmed from ferry propeller wash that stirs up sediments and scours eelgrass beds, construction, and the use of traditional pilings, which would increase shading through a food chain involving mussels, barnacles, sea stars and crabs.

With eelgrass most prevalent in shallow waters, the dock was engineered to jut further into deep water to minimize prop wash. A narrower dock design kept shade to a minimum in the shallow areas. Glass block along the terminal’s walkways allows light though the structure, while white paint below the terminal’s decking reflects the light to keep the area bright.

Keeping things bright is good for the eelgrass and for salmon. Thom said while habitats for juvenile salmon are still being studied, an early test showed they tend to avoid light to dark transitional areas. By maintaining a bright area along their migration path, young salmon are more likely to continue on the path they started.

Wood pilings are being replaced with concrete pilings to help eliminate what scientists refer to as the reef effect, in which crabs denude plant life at the edges of the eelgrass meadows by depositing uneaten shells and debris.

In addition to protecting salmon habitat, Battelle engineered a rock pile south of the dock to promote kelp growth for rockfish habitat.

Russ East, a terminal engineering director for Washington State Ferries, said this week the department is pleased with the eelgrass project.

“So far we’ve achieved what we needed to,” he said. “From a performance standpoint, we’ve been able to successfully operate a ferry terminal while protecting salmon habitat. All the reports I’m getting is that the eelgrass is performing as we expected.”

With this success comes costs. East said additional construction costs to avoid or mitigate environmental impacts during both expansion phases cost $5.3 million. Eelgrass transplanting and site monitoring through 2013 is expected to cost at least $2 million, although that figure could change.

Balancing costs in the name of restoration and utility is wise, according to Thom, who said protecting habitat up front is less costly than attempting to restore habitats once they’re gone.

Thanks to the restoration effort, was an estimated 7,000 square feet of habitat was saved.

Built into the Clinton dock’s engineering plan is long-term cost efficiency. Using reflective white paint below the dock removed the need for expensive high maintenance lighting. Fewer concrete piers require less maintenance, and by transplanting the eelgrass, engineers are encouraging ecosystem processes to continue without human intervention.

East said what makes Clinton an exciting restoration project is that it’s the first of its kind in size and density, and will be used as a model for future Puget Sound ferry terminal projects.

Restoration efforts and monitoring will continue through the expansion’s second phase, with more eelgrass transplanting planned at the expansion’s completion. Battelle is contracted to monitor the site for at least a decade.

Battelle, a Columbus, Ohio-based nonprofit international research firm, has been operating a lab in Sequim since the mid-1960s.