The American Lung Association says breathing in the acrid smoke can be especially harmful to people with asthma or COPD. Children should also avoid the smoke.
Many of the stores at Seaport Village noticed fewer customers. Several closed early.
"I've been coughing a little bit this morning and I definitely had customers come in here coughing and then they're just kind of in and out," said Blair Calhoun, an employee working in Seaport Village Friday.
Exactly what is burning inside the boat is unclear. U.S. Coast Guard San Diego is taking steps to protect the water with a floating boom. The boom is supposed to keep toxic materials from spreading farther into the bay.
"It is a bummer, this is our first time here, hopefully, they get it cleared up," Lathem said.