The tribe, Washington Environmental Council and Puget Soundkeeper on Wednesday issued a notice of intent to sue the Navy over alleged Clean Water Act violations.
The Navy began scraping the hull of the decommissioned USS Independence this month. The Navy is preparing to tow the 1,070-loot-long carrier from Bremerton to Texas, where it will be dismantled sometime this year.
The tribe and environmental groups joined state and federal pollution regulators in expressing concerns that the cleaning was releasing toxic levels of copper-based paint into the inlet.
"Copper is one of the most toxic heavy metals to fish and particularly to salmon," said Chris Wilke, Soundkeeper's executive director. "It's so serious that our state has moved to phase out its use in all boat paint."
The tribe has raised concerns over hull scraping several times.
"We do not believe they should be exempt from regulations that other vessel owners routinely follow," Suquamish Chairman Leonard Forsman said.
Hull cleanings are typically conducted in a drydock facility with pollution prevention and waste disposal capabilities. The Navy began its cleaning without Clean Water Act permits and in violation of federal pollution discharge rules, the tribe and groups allege.
Navy officials say they can claim exemptions to many state and federal pollution rules.
The inlet is on the Clean Water Act's list of impaired waters. Considered one of the state's most polluted areas, the base was designated a federal Superfund cleanup site in 1994. Marine sediment samples taken near the base contain elevated levels of copper, mercury and other heavy metals.
The Navy is removing a 3-inch layer of barnacles and other marine growth from the carrier's hull to comply with rules limiting the spread of invasive species.
"As part of this process, a team of highly skilled divers are gently scrubbing marine growth on the hull of the ship in order to prevent the possible transfer of invasive species," Navy spokeswoman Colleen O'Rourke said in a statement Wednesday. "The objective of the cleaning is only to disturb the reproductive capability of the marine life on the hull, not to remove the biological material or paint."
She declined to comment on the pending lawsuit.
The U.S. Environmental Protection Agency and the state Department of Ecology have urged the Navy to develop a more robust pollution monitoring plan for hull cleaning in Sinclair Inlet. Ecology might ask the Navy to clean portions of the inlet if increased levels of copper and other contaminants are found.