A fence was put up this summer because of the construction work going on at the school. It was locked when firefighters arrived, causing a bit of a delay, but once they got through, they were able to put out the flames rather quickly.
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The thick black smoke even surprised firefighters, who thought they were going to have a tough one on their hands.
"I can tell you coming out here I was expecting a lot worse," said Marinwood Fire Chief Tom Roach. "There was a big column of black smoke which was engulfing the whole valley."
But crews got a handle on the fire not too long after they arrived.
San Rafael's Dixie Elementary is getting its roof replaced, and that's where the fire started -- on the roof of Building A, which houses four first grade classrooms.
Second grader Colin O'Brien was in Building A last year. "I thought it was going to be fine, but I don't think it's going to be fine anymore," he said.
The fire department says most of the damage is confined to the roof but there is some water and smoke damage to the inside.
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The district says it's too soon to tell whether the classrooms will be ready by the start of the school year.
It's a setback for the neighborhood, which was excited about the improvements to the school.
"I just felt really sad for the school because I grew up here and I love the teachers," said former student Georgia Lee.
"This is our community school. This is our world that we live in, right here, so this is -- it's sad," said parent Allyson Kurth.