PORT GAMBLE — There’s a lot you likely have seen in the efforts to improve the health of Port Gamble Bay: Pope Resources’ cleanup to date of the former mill site. The Port Gamble S’Klallam Tribe’s removal of debris from its shoreline. The removal of the Point Julia pier. The North Kitsap Forest & Bay project’s acquisition of 1.5 mile of shoreline, now maintained as Port Gamble Heritage Park.

But there’s a lot more out there you can’t see, under the surface of the water, and that’s the focus of the cleanup effort that begins in July.

Wood waste from 140 years of milling activity is 20 feet deep in places. Those creosoted pilings sticking up out of the water? There are 4,000 more under water, according to the state Department of Ecology, and their removal will be the largest piling removal project in the Puget Sound region, according to Clay Keown, permit administrator for Ecology.

Ecology officials say chemicals from pilings and wood waste have created a hostile environment for shellfish and finfish that call the bay home — and for the people who depend on shellfish and finfish as part of their diet and economy. The bay is also prime spawning habitat for Pacific herring, an important forage fish for salmon; Ecology is working to determine if the herring stocks here are distinct, or if they are part of the so-called Quileute stock.

Sediment and shellfish-tissue samples revealed such chemicals as arsenic, cadmium, chromium, copper, dioxin/furan compounds, PCBs, and carcinogenic polycyclic aromatic hydrocarbons.

Port Gamble Bay is one of seven priority bays identified for cleanup under the Puget Sound Initiative. The initiative was established to coordinate efforts to restore and protect the health of Puget Sound by 2020.

Getting to this point where the cleanup can start took more than a decade of determining the extent of the cleanup (approximately 78 aquatic and tideline acres), who is responsible (Pope Resources, whose predecessor, Pope & Talbot, operated the mill; and the state Department of Natural Resources, which owns the aquatic lands); and from where the money would come.

“We’ve been working on this project for 12 years. We’ve reached a point where we’ve turned a huge corner [and are ready to start],” Keown said.

The cleanup is estimated to cost $20 million, with the costs shared by Pope Resources and DNR. How much will be shared by whom is the subject of a lawsuit filed in Superior Court by Pope Resources. The case is titled “Pope Resources LP et al v. the Washington State Department of Natural Resources, case number 14-2-02374-1.

At a public meeting May 27 at Port Gamble’s Hood Canal Pavilion, Department of Ecology staff members outlined how the project will proceed.

In June, a contractor will determine the best methods for removing the pilings, which are of varied age and condition. In July, the piling removal will begin. The work will be conducted in two windows: July 2015 to January 2016, and July 2016 to January 2017. Hours: 7 a.m. to 10 p.m. Monday through Saturday, with periodic nighttime and Sunday work.

By the time the project is completed, 6,000 creosote-coated pilings, overwater structures, and 70,000 cubic yards of wood waste and contaminated sediments will have been removed. Wood waste located close to shore will have been dredged and remaining areas contaminated by wood waste capped with clean material. Eelgrass, which provides shelter for Pacific herring and crab, will have been transplanted in the cleaned areas. Water quality will be monitored for 10 years.

Ecology representatives said there will be noise and traffic associated with construction. John Kuntz of Olympic Outdoor Center expressed concern about his ability to safely conduct kayaking expeditions out of Port Gamble during the cleanup. Facing the prospect of having to temporarily relocate, he said of the cleanup, “I’ve been in support of this for a long time.”

Before the meeting, the Port Gamble S’Klallam Tribe issued a statement regarding the cleanup:“The Port Gamble S’Klallam Tribe has a significant cultural, spiritual, and economic connection to Port Gamble Bay. The bay connects the Tribe to their ancestral home and is an irreplaceable and productive source for finfish and shellfish. Tribal members practice their treaty rights by harvesting from the bay and surrounding waters year-round for ceremonial, subsistence, and commercial purposes.

“The Port Gamble S’Klallam Tribe has been involved in bay cleanup planning for years and are very happy to see the cleanup move forward. It is the Tribe’s hope that the cleanup will proceed in a manner that will have minimum adverse impacts to Tribal treaty fish harvesters and consumers.”

In the Treaty of Point No Point in 1855, the S’Klallam reserved the right to fish and harvest resources in their usual and accustomed areas. From 2008-12, according to the Tribe, more than 100 Port Gamble S’Klallam Tribe members earned all or a portion of their livelihood working as commercial salmon fishermen; approximately 50 earned all or a portion of their income as commercial geoduck harvesters; more than 150 earned income participating in commercial shellfish harvest, which includes clams, oysters, crab, and shrimp; and 178 exercise their subsistence harvest rights on an annual basis.