The California sea lion, dubbed King Neptune, was put down after tests determined that his condition had deteriorated significantly, officials with the Marine Mammal Center in Sausalito said.
An infection from the gunshot wound had spread to his chest, causing a serious case of pneumonia to develop. The wound was also failing to heal and muscles along his spine were atrophying, a center spokeswoman said.
King Neptune, a young adult male, was rescued from the wharf Aug. 17 after he was spotted by a member of the public.
He was lethargic and underweight, and veterinarians at the center's Sausalito facility found that he had been shot by a large-caliber weapon. X-rays showed bullet fragments lodged dangerously close to his spine.
Veterinarians estimate the sea lion was shot a few days before the rescue. He was put on antibiotics and painkillers, but officials reported difficulty in persuading him to eat.
King Neptune is the fourth sea lion suffering from gunshot wounds that the center has rescued this year.
In May, a female pup that had been shot was also rescued from the Santa Cruz wharf but did not survive. The two other pinniped rescues recovered from their injuries and were released into the wild, center spokesman Jim Oswald said.
The center admitted 9 patients with gunshot wounds in 2010, and 19 in 2009.
It is illegal to harm or harass a marine mammal. Anyone with information on this shooting or any other cases of animal abuse or injuries is asked to call the National Oceanic and Atmospheric Administration's Office of Law Enforcement at (831) 647-2127.