The Suffolk County Water Authority’s unionized workers, without a contract for more than three years, have agreed to a new $40 million contract that will give them pay hikes totaling more than 25 percent over a decade, but with major work rule and health concessions to save money.

The new pact will give workers 2 percent annual pay hikes from 2013 to 2016 as well as annual increases of 2 percent in 2017; 2.25 percent in 2018, 2.50 percent in 2019, 2.75 in 2020 and 3 percent in 2021 and 2022.

The new agreement, however, also will require new employees to pay a 15 percent share of health insurance costs. It also changes work rules to make it easier to assign and schedule crews to do repair work, which officials say will save hundreds of thousands of dollars annually.

“We’re glad it’s finally over,” Jeff Szabo, the authority’s chief executive officer, said Friday, referring to the 55 negotiating sessions it took to reach a deal. He said the new contract meets the board’s goal of “paying a fair wage to our hard-working employees” while “gaining greater work rule efficiencies . . . and health contributions from new employees” to save money.

Szabo said that retroactive paychecks will be sent out by Dec. 15. He said a typical authority union employee who makes about $67,000 a year will receive retro-checks totaling $5,280. Union members also will get a $500 signing bonus.

“It’s been a long time coming, but it was absolutely worth the wait,” said Nick Caracappa, president of Utility Workers of America Local 393. “A lot of good things will come out of this contract because we’ve been able to find common ground on many issues.”

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The authority’s 340-member Local 393 ratified the pact on Thursday in a 264 to 12 vote. The authority’s five-member board is expected to vote on the contract at its meeting Monday night in Oakdale. At the same time, the board is expected to vote on a resolution to require newly hired management employees to also pay a 15 percent share of health insurance costs.

Authority officials say health concessions from both union and management employees are expected to save about $3 million through the remainder of the contract. An employee with the family plan will have to pay $3,700 on a health plan that costs $25,000.

Officials also said the contract does away with written work rules, dating back as far as 40 years, that had previously detailed the size of crews needed to perform different kinds of repair work, rules that often caused delays and were outdated because of new technologies.

The new contract also allows the authority to schedule customer service technicians to work a Sunday to Thursday schedule, to give the authority seven-days-a-week coverage.