BARBARAELLEN KOCH PHOTO | Suffolk County Dredge in the mouth of the Miamoque Canal in Jamesport Thursday afternoon.

The dredging window is now closed for most of Southold’s creeks, and Suffolk County’s annual dredging operation has moved on to Riverhead Town, where workers had just two creeks to dredge before the season closes on Jan. 15.

As of Jan. 6, dredge operators were working on Miamogue Creek in South Jamesport, after finishing work on East Creek earlier in January, said town engineer Ken Testa.

Those two creeks were the only ones deemed of concern to Riverhead Town, Mr. Testa said. Although both Meetinghouse Creek and Case’s Creek in Aquebogue are in need of some dredging, he said, the county doesn’t yet have permits for Meetinghouse Creek.

Case’s Creek can’t be dredged until a bulkhead at Dreamer’s Cove Motel is replaced.

“The county feared the bulkhead could collapse,” said Mr. Testa. “We need the motel owner to replace the bulkhead. They’re working on that now. I think they intend to replace it before the next dredging season.”

The county’s dredging schedule made news last December when Southold Town agreed to pay county workers overtime in order to finish as many creeks as possible before the dredge window closed Dec. 15. Dredging season ends either Dec. 15 or Jan. 15, depending on whether the area is considered prime winter flounder breeding ground.

Creeks with earlier deadlines tend to provide better environments for flounder spawning. Though some in Riverhead expressed concern at the time that Southold would receive preferential treatment because they were paying overtime, Mr. Testa said Riverhead is often the last place to be dredged, in part because the dredge windows tend to close later there.

“Normally, the county starts on the south side and works its way around to Riverhead,” he said. “In order for the county to schedule Riverhead, they initially had to limit number of creeks they’d dredge in Southold. But Southold paid overtime to reach the additional creeks, so as not to push us off our schedule, which was always in place.”

County workers managed to dredge Corey Creek, Budd’s Pond by the Port of Egypt marina and Jockey Creek, all in Southold, and Richmond Creek in Peconic before the Dec. 15 closing, said town Trustee Dave Bergen, who is coordinating dredging for the town.

Mr. Bergen said the county received an extension of the window in order to dredge Little Creek in Cutchogue during the last few days of 2011 and managed to dredge a small section of the entrance to Gull Pond in Greenport on the crew’s last day in Southold Dec. 30.

“It had closed in on the eastern side,” he said. “It was navigable, but only one boat wide. It was a fairly easy project.”

Mr. Bergen said next year he expects the county to focus on creeks on the west end of Southold.

“You get done with one season and you’re already starting to think about the next one,” he said.

byoung@timesreview.com