Well before it was warm enough to plant seedlings in the ground, farmer Micah Barritt began nursing crops like watermelon, eggplant and tomatoes—eventually transplanting them from his greenhouse into rich Vermont soil, hoping for a bountiful fall harvest.

Within a few hours last week, those hopes were washed away when flood waters inundated the small farm, destroying a harvest with a value he estimated at $250,000. He still hopes to replant short-season crops like mustard greens, spinach, bok choy and kale.

“The loss of the crops is a very tangible way to measure the flood, but the loss of the work is hard to measure,” said Mr. Barritt, one of five co-owners of Diggers’ Mirth Collective Farm in Burlington, Vermont. “We’re all grieving and heartbroken because of this.”

That heartbreak was felt by farmers in several Northeast states after floods dealt a devastating blow at the worst possible time, when many plants were too early to harvest, but are now too late to replant in the region’s abbreviated growing season.

Storms dumped up to two months’ worth of rain in a couple of days in parts of the region, surpassing the amount that fell when Tropical Storm Irene blew through in 2011, causing major flooding. Officials have called last week’s flooding Vermont’s worst natural disaster since floods in 1927.

Diggers’ Mirth is one of seven commercial organic farms located at the Intervale Center, according to Melanie Guild, development director of the center, which manages 350 acres in the heart of Burlington.

Operators of the center, located near the Winooski River, have long been aware of the threat of flooding. As the forecast called for heavy rains, the center reached out to hundreds of volunteers to harvest as much as possible.

“This is smack dab in the middle of the growing season so anything that was ready to harvest was pulled. Whatever was left was lost,” Ms. Guild said. “There were cabbages just floating around in the flood.”

All seven farms were washed out. Losses will likely run higher than Irene, where losses tallied about $750,000, she said.

Not all farms that suffered losses grew vegetables or flowers.

The Maple Wind Farm in Richmond Vermont, which produces pasture-raised animals, was also struck.

Beth Whiting, who owns the farm with her husband, said even with predicted heavy rains they assumed their turkeys would be OK because they’d never seen flooding reach the area where they kept the birds.

Then at about 3:30 a.m. on July 10, the nearby Winooski River crested higher than they’d ever imagined, Mrs. Whiting said. Workers in a canoe were able to rescue about 120 of 500 turkeys. Workers also saved about 1,600 chickens, but lost 700 at a second farm.

“We had no idea the flood was going to be so dramatic,” she said.

The flooding forced many farmers into tough choices, according to Vermont Secretary of Agriculture Anson Tebbetts. Dairy farmers who found roads to processing plants impassable were forced to dump milk.

Another problem is the loss of corn, a key source of food for the dairy industry. Thousands of acres were completely or partially underwater or flattened and unusable, he said. Flower farms were also destroyed.

“Some blueberry bushes are under water. That is very important for pick-your-own operations. Once produce is underwater it can’t be used,” he said.

As of the end of last week, Vermont farmers had reported 7,000 acres in crop damage, Mr. Tebbetts said, adding many farms must clear debris washed onto their fields when rivers overflowed.

In Massachusetts, at least 75 farms have been hurt by flooding, with about 2,000 acres in crop losses at a minimum value of $15 million, according to the state Department of Agricultural Resources. That number is expected to climb as more damage is assessed and the longer-term impacts set in.

Damaged farms ranged from community farms to a farm with 300 acres of potatoes that were a total loss just weeks from harvest to a 230-member “community supported agriculture” farm only five weeks into a 30-week program.

Massachusetts Gov. Maura Healey said the disaster requires an unprecedented effort to chase federal, state and private money. On Thursday she announced a Massachusetts Farm Resiliency Fund, a partnership between philanthropic organizations and private foundations.

“It’s just such a shame,” Ms. Healey said after touring flooded farms this week. “Unlike Irene, this happened right on the cusp of harvest, so the crops are ruined for this year.”

In Connecticut, Bryan Hurlburt, the state’s agriculture commissioner, said the flooding impacted about 2,000 acres of farmland, much of it in the Connecticut River valley.

The flooding is part of a larger environmental crisis, according to Connecticut Gov. Ned Lamont.

“What the hell is going on here?” Mr. Lamont said, speaking in front of a flooded farmer’s field in Glastonbury. “Look behind us. We were irrigating that a couple of months ago, desperate for water in the middle of a drought. And today it’s Lake Wobegon. And so what do you do?”

Kate Ahearn, who runs Fair Weather Growers along the Connecticut River in Rocky Hill, said the flood waters took a heavy toll.

“This is our livelihood that is at stake,” she said. “Fair Weather Growers is going to lose about 300 acres of crops and more than half of our labor force, plus all of our wholesale accounts.”

In Pennsylvania, officials have been monitoring rainfall.

“When water is rising, that’s the big concern because you get a lot of standing water and the soil starts to loosen up, turns into mud and the mud starts to wash away. When dirt and soil washes away, crops do as well,” said David Varner from the Pennsylvania Farm Bureau.

Recently, a farmer called the Penn State Extension in Bucks County saying his crops looked wilted, as if they hadn’t been watered in a while, said Margaret Pickoff, horticulture extension educator.

It was the opposite: The soil was so full of water, the plant roots were unable to take in any oxygen, and were dying off.