Sky7 video from Wednesday afternoon shows the fuel spread from Alameda all the way to the Oakland estuary.
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"This is an active incident with the U.S. Coast Guard and they're doing their best to mitigate any of the runoff, any of the flotation of petroleum or hazardous fluids that may be on the water surface," Alameda Fire Department Division Chief James Colburn told ABC7 News.
The spill also disrupted neighbors who live nearby.
"This morning I walked out my door at 10 am and was just inundated with a fuel smell," Liz Williams who lives in a houseboat on the marina said. "When I looked at the water there was a rainbow sheen I could see the fuel was covering most of the water."
An inspector with the California Department of Fish and Wildlife described the spill as "minor to moderate."
"What you can see on the water is kind of deceptive," Robert Chedsey, an oil prevention specialist, explained. "A little bit of oil on water goes a long way and it spreads out very quickly."
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Chedsey said it's hard to collect this amount of fuel and that the most effective clean up is natural evaporation.
Williams said she thinks more can and should be done.
"We're in this climate change reality," she said. "It goes somewhere. It drops down into the water, it evaporates into the air. It goes somewhere. It's not like this becomes a non-event. That's what I'm finding difficult about this explanation."
Chedsey said the boat holds 250 gallons of oil but they do not believe all of that went into the water. They also have so far not seen any impact on wildlife.
Officials say the boat owners are cooperating and, as is required of them, are covering the cost of the clean-up. The cause of the fire is still unknown.