"It could be starting to affect them."
Apple crops had not been damaged by the rain, but David Goodsell from Kelston Orchards said colder weather was better for the fruit.
"The weather being quite warm doesn't develop the colour we would like," he said.
"Ideally we would like cold, dewy nights followed by a nice sunny autumn day."
The crops were largely unaffected by either the recent rain or the summer drought, Mr Goodsell said.
Hawke's Bay orchardists were lucky to have good irrigation systems and water supplies, he added.
Continued heavy rain could become a problem for apple growers because eventually it would damage the crop, causing splitting and other problems.
While many orchards have been largely unaffected by the bad weather, those growing grapes and onions were not so lucky.
Mr Goodsell expressed sympathy for onion growers and winemakers who were particularly affected.
"My heart does go out to other growers," he said.
Anya Thomas, managing director of NZ Growers, said many onion crops in Hawke's Bay were affected by the rain but not all varieties.
"It's not completely non-salvageable," she said.
Some types of onion were harvested before the rain started, but many of the main varieties were not.
"In an ideal world, you would want to be harvesting in the sunshine," Ms Thomas added.
Onion growers in Pukekohe and other North Island areas were also affected by heavy rain.
The amount of damage to onion crops in Hawke's Bay and other regions is unknown.
"A lot of growers won't know until they actually get their crop in," Ms Thomas said.
Over the weekend, 21.4mm of rain fell in the Napier area and 13mm in Hastings.
The rain is set to continue until Thursday, and resume next week after a fine weekend.
MetService issued a severe weather warning for Hawke's Bay yesterday, with more heavy rain expected overnight.