The Fairfax County Board of Supervisors on Tuesday voted unanimously to boost the pay of about 11,000 county employees by 2 percent, the first such raise for its staff in three years.

The board also agreed to put aside nearly $29 million because of another large, anticipated budget gap next year and the likelihood of having to pay for damage caused by the recent flooding.

The pay raise, proposed by Chairman Sharon S. Bulova (D), takes effect Sept. 24 and will cost about $15 million in fiscal 2012, which began July 1.

Earlier this year, while enacting a $6.1 billion budget, the board conditionally agreed to grant employees a 1.52 percent raise, at a cost of $11.3 million.

Better-than-expected sales tax revenue, deeper cost-cutting by agencies and other unexpected savings, such as the favorable settlement of an $8 million lawsuit, allowed the board to sweeten the pay package with an extra $3.7 million.

Although less than the 3.5 percent raise several public employee unions had sought, the 2 percent increase was still welcome in the ranks.

“We’re very pleased,” said Karen Conchar, president of the Fairfax County Government Employees Union/Service Employees International Union (FCGEU/SEIU). The union had launched a “Drive for 3.5” campaign to match the raises the Fairfax County School Board gave teachers.

The board, after hearing that county employees’ pay has slipped relative to their peers in surrounding jurisdictions and the private sector, also indicated interest in enhancing compensation in the next budget. That could pose a challenge, however: County Executive Anthony H. Griffin said Tuesday that Fairfax faces a budget gap of as much as $120 million next year, partly because of the need to boost school funding by 5 percent to cover previously adopted increases in teacher pay.

Tuesday’s pay raise was enacted as part of an annual exercise by the board — known as carryover review — to consider how to use money left over from the previous fiscal year. About 20 people stepped up to the podium to share their views of how to spend the money at a meeting that normally would have only a handful of speakers.

Public-employee unions urged supervisors to uphold their pledge to use any leftover funds for raises. Several noted that their pay has been frozen for three years even as the cost of living has risen, especially for energy, health care and food.

“These sacrifices have taken a toll on us and our families,” Conchar said. She told the board that Fairfax employees now earn less than peers in Alexandria and Arlington and Prince William counties. County employees also earn about $12,000 less than those who perform comparable duties in the private sector, she said.

Randy Creller, chairman of the county’s Employees Advisory Council, which represents county and schools employees, asked for 3.5 percent pay increases, saying that would help make up for the 15 percent lost since a pay freeze began with the passage of the fiscal 2010 budget.

Others urged redirecting the money toward parks or human services. Del. Scott A. Surovell (D), who represents a district along the Route 1 corridor, suggested that the county use some of the money to reduce waiting lists for day care and preschool.

Others urged the county to bank the money.

“My message is simple: Save. Don’t spend,” said Carey C. Campbell, an independent candidate for the Board of Supervisors’ seat in the Braddock District. “If you must spend, spend wisely.”