An agreement between Seattle City Light and the state Department of Ecology will remove legal uncertainty over water use for hundreds of homes in parts of Skagit and Snohomish counties.

Through the agreement announced last week, Ecology is buying some of Seattle City Light’s senior water rights, said Ecology Water Resources Program Regional Supervisor Rita Berns.

Seattle City Light will then continuously release 0.5 cubic feet of water per second from Gorge Dam — the lowest of three hydroelectric dams on the Skagit River — specifically to offset the impact on the river by the use of area wells. Berns said that release is enough to cover a half-square-mile with 1 foot of water each year.

That will enable Ecology to provide uninterrupted water rights for homes with wells built between April 2001 and October 2013 and affected by the 2013 Supreme Court decision regarding the Skagit River instream flow rule.

The decision left those homeowners without an uninterruptible source of water and other landowners without the ability to build homes.

Ecology is paying $1.1 million for the right to that water and $315,000 for the yearlong development of the agreement.

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Berns said the water right will offset water use for about 400 homes built during that time in the Skagit River watershed, which covers most of Skagit County and extends south into Snohomish County along the Sauk River.

About 60% of the water will be designated for those existing homes and 40% for new construction in a limited area along the Skagit River, according to the agreement.

Seattle City Light holds water rights to store water behind its three dams. It is also required, under federal permit, to maintain flows favorable for fish downstream.

The water right Seattle City Light is selling to Ecology is a fraction of its water storage capacity, according to the utility’s website.

In order to release 0.5 cubic feet of water per second continuously, Seattle City Light needs to complete a Gorge Dam infrastructure project, which is expected to begin this fall.