After more than a year of contention and a lawsuit over the contractor’s workmanship in building the new La Conner Middle School, the issue has been settled.

The school opened in September 2015, but the district did not accept the project as complete and withheld close to $700,000 of the $11.48 million contract amount, saying there were construction deficiencies.

The contractor sued the school district in April.

A settlement agreement signed by the school board on Monday requires the contractor, Steilacoom-based BNCC, to fix all the deficiencies and requires the school district to pay $340,000...