The adult male died between 9:30 and 10 a.m., said Julika Wocial, rescue program supervisor for the foundation.
"We're going to conduct an examination of the animal to hopefully find out some clues as to why it died," she said. "We really don't know why it expired."
Wocial said she doubted scratches and abrasions the dolphin suffered as it came ashore contributed to its death. "That happens when dolphins come ashore," she said. "Those were minor."
She said, however, the dolphin, known as a common dolphin, had "elevated breathing" throughout the night and never swam normally.
"It was always in a critical condition," she said.
Rob DiGiovanni, senior biologist and director of the Riverhead foundation, said the survival rate in cases where dolphins come ashore is roughly 10 percent.
"It's a really big hurdle to get over once you have the animal in rehab," he said earlier Friday. "There are a lot of factors, not the least of which is the cause of the stranding and the stress of the rehab itself."