Neighbors reported seeing the dead fish popping up in mass amounts over the weekend.
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"We're seeing them around the circumference of the lake, the lake's just about three miles around, so we're going to be going all the way around because we're seeing reports from the community about observing this phenomenon around this whole lake," Sean Maher, a spokesman for the Oakland Public Works Department said.
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Maher says it's coming from a regional algae bloom, impacting miles of shoreline in the East Bay.
It was harmful enough for the city to caution people to stay out of the water and to keep their pets out of the water too.
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But it wasn't until this past weekend when they started to see a significant level of fish and wildlife die off.
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The environmental watchdog group, San Francisco Baykeeper, says not only does the algae emit a fish toxin, it is associated with a biological event that sucks the water of oxygen, which kills off even more fish.
"The city of Oakland's Public Works Department maintains and cleans and beautifies our public spaces for the community," Maher said. "We're out here making sure that we're abating and cleaning up these dead fish and wildlife, anticipating hot weather over the weekend, wanting to make sure it's a welcoming and comfortable place for folks to be."
He says it took a few days to get crews out to the lake, just to make sure the work they're doing complies with requirements of Lake Merritt being a national wildlife refuge.
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The goal is to finish the cleanup by the end of the day on Wednesday.
But what doesn't get done, Maher says they'll come back to finish on Thursday.