MORGANZA, Louisiana (Reuters) - Army engineers on Saturday opened a key spillway to allow the swollen Mississippi River to flood thousands of homes and crops but spare New Orleans and Louisiana's capital Baton Rouge.

The Army Corps of Engineers opened one of the 125 floodgates at the Morganza Spillway 45 miles northwest of Baton Rouge shortly after 3 p.m. CDT, sending a flume of water onto nearby fields.

The move, last taken in 1973, will channel floodwaters toward homes, farms, a wildlife refuge and a small oil refinery in the Atchafalaya River basin to avoid inundating Louisiana's two largest cities.

Weeks of heavy rains and runoff from an unusually snowy winter caused the Mississippi River to rise, flooding 3 million acres of farmland in Mississippi, Tennessee and Arkansas and evoking comparisons to historic floods in 1927 and 1937.

It could take three weeks for the enormous flow of water to pass through a system of levees and spillways to the Gulf of Mexico about 100 miles to the south, said Major General Michael Walsh, president of the Mississippi River Commission.

"It's putting tremendous pressure on the entire system as we try to work this amount of water through the Mississippi River tributaries," Walsh told reporters before the floodgates opened.

Some 3,000 square miles of land could be inundated in up to 20 feet of water for several weeks. When flows peak around May 22, the spillway will carry about 125,000 cubic feet per second, about one quarter of its capacity.

About 2,500 people live in the spillway's flood path, and 22,500 others, along with 11,000 buildings could be affected by backwater flooding -- the water pushed back into streams and tributaries that cannot flow normally into what will be an overwhelmed Atchafalaya River.

Some 18,000 acres of cropland could be flooded as waters rise, hitting their crest in about a week and remaining high for several weeks before subsiding.

"The land's going to wash away, but that's life," said Hurlin Dupre, who represents Krotz Springs on the St. Landry Parish Council. "The worst of it is we are in a drought and we can't use none of that water."

PROTECTING NEW ORLEANS

Failing to open the spillway would have put New Orleans at risk of flooding that, according to computer models, would eclipse that seen during Hurricane Katrina in 2005, when 80 percent of the city was flooded. About 1,500 people died in the disaster.

In addition to threatening densely populated areas, lower Mississippi flooding threatened as many as eight refineries and at least one nuclear power plant alongside the river.

The refineries make up about 12 percent of the nation's capacity for making gasoline and other fuels.

In the Atchafalaya River basin, authorities went door to door to begin evacuations in small towns and parishes in the path of the water, which could take weeks to reach the Gulf of Mexico.

Louisiana Governor Bobby Jindal said on Friday the state had plans with the American Red Cross to provide shelters for evacuees.

"I'm very scared," said Heidi Fangue, a Morganza resident. "I have my bags packed and ready to go."

Fangue, who was selling T-shirts that read "Morganza Spillway 2011 -- Gates finally opened," said she would depart in her mother's camper once floodwaters began to creep over the nearby levee.

In Morgan City to the south, workers were reinforcing levees and placing sandbags along the Atchafalaya River.

"The fatigue factor is something we'll have to watch for, both on the levees and on the people," Morgan City Mayor Tim Matte told Reuters. "This is unprecedented."

The Corps said the gradual opening of the spillway's gates would prevent an immediate rush of water. Alon USA Energy said it expected its 80,000 barrel-per-day refinery in Krotz Springs to be surrounded by water within 10 to 14 days of the spillway being opened.

Exxon Mobil's 504,500 barrel per day (bpd) refinery in Baton Rouge, the nation's second-largest, was not expected to cease operations, but its Mississippi River dock was shut due to high water, a plant spokesman said.

(Additional reporting by Erwin Seba in Houston, Writing by Chris Baltimore; Editing by Paul Simao)