TIM KELLY PHOTO | Flood waters from West Creek in New Suffolk pouring onto the low-lying field at the Wickham Fruit Farm on Monday.

Hurricane Sandy, which flooded many areas along the North Fork with water from the Long Island Sound and the bays on Monday, struck so late in the season that most farms had already harvested their high value summer crops.

But at least one area farmer is now having to deal with salt from the sea left on his farm.

Cutchogue farmer Tom Wickham is one of the closest farmers to salt water on the North Fork.

During the hurricane, a tree on top of the dike his family built to protect fields from neighboring Wickham Creek toppled over, causing the dike to erode further as salt water poured onto his fields.

By high tide Monday night, he said, there were three feet of water on his fields.

A field of 600 small apple trees planted in a low area on the edge of the creek this spring saw the most extensive damage, and Mr. Wickham said Friday he isn’t sure whether it makes more sense financially to transplant the trees to a drier spot or to start over with new trees.

“They’re not toast yet, but there’s no way they will survive in that environment,” he said. “Whether it makes economic sense to transplant them or to buy new trees, I’m not sure.”

He said he won’t be able to replant anything in the spot where those apple trees were for three to five years because of the salt that is now in the soil.

“I never planted tree crops in the low lying fields before,” he said. “But I knew they would grow well there.”

Mr. Wickham said he believes between 1,000 and 2,000 other trees on his farm were exposed to salt water.

“We have to do soil sampling to find out how deep the salinity is,” he said. “Some parts washed over and it wasn’t really standing water. Maybe those fields will be salvageable.”

“Our season basically finished up at Halloween,” said Jeff Rottkamp of Rottkamp’s Fox Hollow Farm in Baiting Hollow. “Had this been two months ago, we would have had a disaster.”

More than a year ago, Tropical Storm Irene hit the North Fork, knocking over crops and — more damagingly — whipping up salt water from the sea onto planted produce. It will take about a week or so to see how bad the salt spray from Sandy is, Mr. Rottkamp said, but since most crops were already harvested, the effects will not be as economically devastating.

At Schmitt’s farm stand on Sound Avenue, Debbie Schmitt was just opening up shop Thursday afternoon after power was restored. She said corn had been knocked over and the delicate herbs like cilantro and arugula were ruined by the storm, but otherwise the farm escaped without much damage.

“We’re a lot luckier than a lot of other people,” Ms. Schmitt said.

Mr. Wickham said he hasn’t yet looked seriously into obtaining relief funding from the government.

“I’m focused on trying to put the dike back together,” he said. “Even today, salt water is still coming in and going back. We’ll do it by this weekend, but it may not be a permanent job.”

Additional reporting by Paul Squire.