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Nearly half of California's water supply gathers in the Sacramento-San Joaquin Delta. From there, it is shipped to cities and farms using massive water pumps and a system of aqueducts hundreds of miles long. Well, a federal judge has ordered pumping operations to be drastically reduced to protect a tiny, threatened fish, the delta smelt. And that could happen sometime this week. From member station KQED, Tamara Keith reports.

TAMARA KEITH: No one knows how many delta smelt are left. The once prevalent fish is on the endangered species list as threatened. And many fear it's nearly extinct. Every fall, biologists with the California Department of Fish and Game survey the waters of the delta for the first two weeks of each month. On this November morning, the boat hits the water as the sun is still rising. Fog hugs the delta's sunken islands.

(Soundbite of motorboat engine)

KEITH: We're on the Sacramento River right by the town of Rio Vista in the delta. And this is prime delta smelt territory, which is why we're here, because we're trying to find delta smelt, which is no easy task these days.

Dr. DAVE CONTRERAS (Biologist, California Department of Fish and Game): Now, we're ready to throw the net out. Are you ready?

KEITH: Dave Contreras is a biologist with the Department of Fish and Games. The boat tows the net behind it, gathering life from deep under water all the way up to the surface. In 1980, eight biologists pulled in nearly 600 delta smelt in the month of November. Not this year.

dr. CONTRERAS: Look what I found. I caught the illusive delta smelt.

KEITH: This silvery translucent fish, hardly two inches long and skinny as can be, this fish is forcing the cut back of water supplies to 25 million people and millions of acres of farmland. Contreras admits the delta smelt is an unlikely protagonist.

Dr. CONTRERAS: It is kind of a wussy fish, but — so to speak, but, you know, it's pretty important as far as being an ecological indicator. So we need that fish specie around.

KEITH: By the end of the day, the team has captured four delta smelt. It turns out those were the only ones found in the entire month of November. Biologists say this is just one sign of a struggling ecosystem. Short on good habitat, overrun with invasive species and heavily burdened by the demands of California's cities and farms.

(Soundbite of water pumps)

KEITH; The state and federal pumps at the south end of the delta are massive. They were designed to literally reverse river flows while they pull huge amounts of water out of the delta. This time of the year, the pumps are very active. But a federal judge's ruling says water managers have to slow things down during critical times for the delta smelt. Water managers expect the state will have to reduce pumping in the coming year by anywhere from seven to 30 percent.

Mr. BRENT WALTHALL (Assistant General Manager, Kern County Water Agency): This is like a drought, only it's manmade. This is from a court rather than from the skies.

KEITH: Brent Walthall is assistant general manager of the Kern Country Water Agency. They supply farmers in the agriculturally rich San Joaquin Valley with the water they need to irrigate their crops. He says this court ruling to protect the tiny fish is big trouble for the farm economy.

Mr. WALTHALL: Farmers, right now, are playing for the crops they'll plant in January, February, March and April. They are reducing their seed orders, they are reducing their equipment orders, they are laying off folks. So, yeah, in the agricultural community, we feel this immediately.

KEITH: In cities like Los Angeles and San Diego that rely in part on delta water, the impacts won't be quite as immediate. Still, residents are being asked to conserve. Roger Patterson of the Metropolitan Water District of Southern California says his agency will have to pull from reserves that should save for a drought or earthquake.

Mr. ROGER PATTERSON (Assistant Manager, Metropolitan Water District of Southern California): We're in some times like we really haven't seen in California before. I mean, we've had things lined up in a very unusual way.

KEITH: The court ordered water cuts are expected to last through July when the delta smelt normally move out of harms way. But most involved agree that over the long term, the way the delta is managed, is going to have to change.

For NPR News, I'm Tamara Keith in Sacramento.

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