It’s not unusual to see dead fish around the Inner Harbor as summer ends, but several thousand floating in the water Wednesday could be one of the largest fish kills in decade, according to an official from the National Aquarium.

State officials said about 24,000 fish died, mostly juvenile Atlantic menhaden. Other dead fish include catfish, white perch and blue crabs.

Maryland Department of the Environment officials were out on the harbor Wednesday morning to measure water quality. A spokesperson said the water is “essentially depleted of oxygen” and there is no sign of a pollution event.

Jack Cover, general curator for the National Aquarium, called the fish kill “perplexing.”

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“It’s a natural occurrence for this bacteria to do this,” he said, but it’s exacerbated by “the changes in the environment that has been created in the harbor” including stormwater runoff that brings in high levels of nutrients.

Environment department officials spotted several thousand dead fish in pockets from the Rusty Scupper to the Science Center.

“We are at the site and are continuing to assess the geographic extent and magnitude of the fish kill,” Jay Apperson, a spokesperson for MDE, said.

Fish kills typically happens every spring and fall, when water temperatures fluctuate.

“But the magnitude of it, this is the worst I’ve seen in my 37 years working at the aquarium,” Cover said.

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The high temperatures and abrupt, colder evenings made the “perfect storm” for fish kills, Cover said. He said he and other officials at the National Aquarium noticed an algal bloom on Monday, when the water turned brown.

That was likely a mahogany tide, which happens when pollutants and waste runoff high in nitrogen and phosphorus are in the water, causing algae to grow. This is more likely to occur after heavy springtime rain and stretches of warm, dry days, according to the National Aquarium. The more algae that die and decompose, the more carbon dioxide is released in the water, taking up dissolved oxygen.

When days are dry and sunny and the evenings are cold, naturally occurring sulfur bacteria that lives on the bottom of the harbor float to the surface due to changes in water density.

The warm water at the harbor’s surface cools, which causes it to become more dense and sink to the bottom. That pushes the water on the floor of the harbor upward in what is known as thermal inversion.

“There’s all kind of undigested organic material that’s been gathering on the bottom of the harbor,” Cover said.

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The sulfur bacteria, now exposed to sunlight, then performs anoxygenic photosynthesis — essentially, photosynthesis without producing oxygen — which is why the levels of oxygen drop.

Cover noticed blue crabs and fish coming up near the surface on Monday, he said, likely to try to get oxygen. On Tuesday, the bacterial bloom had grown exponentially between Piers Three and Four, he said.

Adam Lindquist, vice president of Waterfront Partnership, said his team noticed the dead fish Wednesday morning when collecting water samples to test for human health indicators.

None of the changes pose any threats to humans, he said, but shows the city should work to reduce environmental stressors. It also indicates the impact of climate change, as summers continue to get hotter and more extreme.

“We really need to do more to reduce runoff and the amount of nutrients in our water waste,” he said.

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As water stabilizes and officials pick up the dead fish, the harbor should clear up within a couple of days, he said.

Cover said the floating wetland exhibit that re-creates a salt marsh habitat could be helpful due to its aerators. The fish in the shallow channel near the new habitat have survived and other animals are approaching it in search oxygen. It can alleviate some stress and provide a “dissolved oxygen refuge,” Cover said.

“Nature reacts to these things, but it’s a little bit disheartening,” he said. Atlantic menhaden are important fish and they are already overharvested for fish oil. Ospreys, or sea hawks, prey on menhaden and are struggling to find food for their young.

“This huge number gone is not moving in the right direction,” he said.

Dead fish were floating between Pier Five and Pier Six in the Inner Harbor Wednesday morning. (Jerry Jackson/The Baltimore Banner)