They ultimately decided to have lifeguards tow the whale to Fiesta Island. A truck then transported it to Miramar Landfill.
"There's a lot of politics with whales on the beach, so one of the things is jurisdiction. In this case we were able to provide mutual aid with the state," Marine Safety Captain Nick Lerma said.
The 26-foot carcass, believed to be that of a juvenile gray whale, was spotted about three-quarters of a mile offshore about 9:30 a.m., according to the San Diego Fire-Rescue Department.
“It looks like it's been dead for a while,'' SDFRD spokesman Lee Swanson said.
NOAA Fisheries Research Biologist Kerri Danil measured the whale and began taking samples with her team Thursday afternoon.
"We can tell approximately how old it is. We can get a skin or muscle sample, which will tell us genetics. We can tell if it's a male or female from the genetics sample, but unfortunately because this whale is so decomposed that's all the information we'll be able to get from it," Danil said.
Her team took photographs in addition to collecting the data before the whale was loaded into a truck and transported to the Miramar Landfill.
Danil said they would not be able to determine a cause of death, but the information they could collect would still be helpful to determine gray whale trends.
City lifeguard officials used a rescue boat to pull the cetacean remains to Fiesta Island in Mission Bay before it was sent to the landfill.
This was the best option, according to Cpt. Lerma, who said had they towed it out to sea, it would eventually just return to the shore and become a foul-smelling problem.
Despite the strong odor, many people gathered along Fiesta Island to catch a glimpse of the whale.
"It's sad," passerby Michelle Lamar said. "I just wonder what happened, why he's here and how he died."