EVERETT — After a nearly monthlong stalemate, the Department of Fish &Wildlife and Native American tribes have come to an agreement on a recreational fishing season for Puget Sound.

The agreement reached Thursday afternoon follows extended negotiations between state and tribal fisheries managers after they failed to reach an agreement earlier this spring.

The state and tribes must now obtain a joint federal permit in order to open the fishing season in Puget Sound waters.

“We plan to re-open those waters as soon as we have federal approval,” said John Long, salmon fisheries policy lead for Fish &Wildlife. “We anticipate getting the new permit within a few weeks.”

Approval of the permit is expected by mid-June. In the meantime, a closure of recreational fishing that was enacted May 1 remains in effect.

The season includes a hatchery chinook season on the Snohomish River from June 1-July 30. A sockeye season on Baker Lake also is planned starting in mid-July, with a maximum take of 4,600 fish for the season.

Many rivers, including the Snohomish, the main stem of the Stillaguamish, the Skagit and the Cascade, will be closed in September and October to protect returning coho.

Details of the proposed new recreational season are posted online at http://wdfw.wa.gov/fishing/northfalcon.

The tribal and state managers now will focus on addressing long-term resource management concerns, such as restoring habitat and boosting salmon stocks.

What that will entail remains to be worked out, said Lorraine Loomis, the chairwoman of the Northwest Indian Fisheries Commission.

“We will work up a plan and see where we can work together to complete the work. It could be restoration, it could be laws,” Loomis said. “What we found out, right now we’re fighting over the last fish, and that doesn’t work.”

Further negotiations need to address long-term changes to the climate as well as restoring habitat, she added.

The process of co-management needs to be reworked, she said.

“Obviously our process is broken and I think we have to figure out why our process is broken and fix it,” Loomis said.

The negotiations have played out against a background of expected low runs of salmon, especially coho, and a resurgence of ill feeling between some recreational and tribal fishing interests.

In April, the Pacific Fishery Management Council released its rules for the marine fishing seasons.

But without an agreement at the state level for the inland waters, including the Strait of Juan de Fuca and Puget Sound, the 20 treaty tribes in Washington pre-emptively closed their own inland coho fisheries.

Then on May 1, the state closed most inland river fishing areas to sports fishermen.

The tribes submitted a separate permit to NOAA Fisheries.

But while that remained unsettled, the federal Bureau of Indian Affairs on May 3 determined that a six-day tribal harvest of a maximum of 1,250 spring-run chinook salmon wouldn’t violate the Endangered Species Act.

Tribal fishermen took to local rivers to catch the first salmon of the season while non-tribal anglers staged protests in LaConner and Lacey.

The permit process won’t be able to move forward until the agency receives the joint application, NOAA Fisheries spokesman Michael Milstein said.

“We’ve been processing the tribal only proposal, because we’ve been working on that we have a pretty good head start on all the analysis we’ll do on this,” Milstein said.

“That gives us hope that we can get it done quickly,” he said.

The ongoing closures include salmon and steelhead fishing in Puget Sound marine areas, and all fishing in several lakes and many rivers that flow into Puget Sound.

A complete list of ongoing closures is available online at http://wdfw.wa.gov/fishing/pugetsound_salmon_update.

Chris Winters: 425-374-4165; cwinters@heraldnet.com. Twitter: @Chris_At_Herald.