First it was rain, then it was golf ball-sized hail – apple farmers in southern New Hampshire say their crop has taken a beating from spring and summer’s crazy weather.

Joan Pratt, co-owner of Apple Annie orchard in Brentwood, said her farm was nearly closed this year because of a freak hailstorm in July.

In 23 years running a pick-your own orchard, Pratt and her husband, Charles, said they have never experienced anything as damaging. Nearly all their crop – 90 percent to 95 percent – will have to be sold as cooking apples, said Joan Pratt.

“Virtually every apple was affected somehow,” she said. “We’ll be making a lot of cider this year.”

Going back further in the calendar, May’s heavy rains and flooding not only did damage to the land, but also made it difficult for bees to pollinate apple blossoms.

“On a national and regional level, the crop is down,” said Peter Wagner, owner of Applecrest Farm Orchards in Hampton Falls. “In New England, apples are down because of the poor spring we had.”

Wagner said orchards in northern Maine and Vermont also are experiencing smaller crops.

With 14,000 trees on about 300 acres, Applecrest is the largest and oldest orchard on the Seacoast. Wagner said Applecrest will have an above-average crop this year, but it had a high price. The heavy rain meant extra money and work to spray and protect the trees with covers.

Agriculture Commissioner Stephen Taylor said all is not lost. Good conditions later in the summer helped many orchards gain ground.

“We had just a perfect lineup – a lot of rain early, the fruit is sized well, big, fat apples, then in August we got some cool nights for some nice color,” he said.