The holdout lasted eight days.
Lynch will not be receiving the new deal and added money he sought, but Seattle is expected to add some financial concessions to his contract, sources said.
Lynch is in the third year of a four-year, $30 million deal. He received $6 million of it in a signing bonus. Lynch will make $5 million in base salary this season and $5.5 million in 2015, but he wanted more money up front or more money guaranteed.
The running back showed up for minicamp in June to avoid a hefty fine, but made a stand with the start of training camp. Lynch is subject to a $30,000 fine for each day of camp he misses. He has accumulated nearly $500,000 in team fines for his holdout through Thursday, but it is unclear if the Seahawks will collect the fines or waive them.
On Thursday, Lynch was caught by television cameras talking on his phone out near the Seahawks practice fields wearing a hooded ``Beast Mode'' sweatshirt and knit cap on an 85 degree day. He was later hanging out in the lobby of the facility.
He must still pass his physical and be added to the active roster. Seattle's roster is currently at the 90-man limit.
Lynch, 28, has been the workhorse of the Seattle offense the past three years, rushing for 4,051 yards (along with 39 touchdowns) on 901 carries. He has averaged 300 carries and 1,350 yards over the past three seasons.
"Obviously, to have a guy like Marshawn back with us, a man who has been to four Pro Bowls, is something we definitely want," Seahawks quarterback Russell Wilson said. "Marshawn is one of those guys who has a knack for playing football. His running ability is unique and one of a kind. He brings whole other level of experience. He's an elite football player."
Last season, only Adrian Peterson had more yards after contact than Lynch's 574, and it was only by a margin of five yards. Lynch ranked first in the NFL in red zone rushing touchdowns last season with 12.
With Lynch away, the Seahawks have let Robert Turbin and Christine Michael get the bulk of carries during camp. That was already going to be the case during the preseason with Seattle wanting to keep Lynch healthy for the regular season opener against Green Bay.
Both Turbin and Michael have been impressive thus far with Lynch gone.
"The more guys that we have the better," Wilson said. "To have a guy like Marshawn Lynch ... is a good thing. We definitely want him on our team for sure."
Information from ESPN.com Seahawks reporter Terry Blount and The Associated Press was used in this report.