Choosing one flood over another, federal officials opened a Mississippi River spillway Saturday for the first time in 38 years, swamping a swath of Cajun country in an attempt to spare the cities of Baton Rouge and New Orleans.

The partial diversion of the river will mean the inundation of thousands of square miles of lowlands, but officials say it is necessary to lower the risk of catastrophe in the big cities downstream.

The situation remains a highly anxious one for the Army Corps of Engineers and for Louisiana’s residents and public officials. The Mississippi is at, or near, record levels all the way up to Illinois because of extreme deluges in the upper Midwest and meltwater from a winter of heavy snowfall.

At 3 p.m. CDT, the Corps opened one bay of the Morganza spillway, creating an instant whitewater river that turned a grassy floodplain, 20 miles long and five miles wide, into another finger of the Mississippi. The water flowed toward the Atchafalaya River, hit another levee and hung a left, heading south, down through the Atchafalaya floodplain.

Parts of six Louisiana parishes now face flood waters in the coming days as the diverted water moves toward the Gulf of Mexico. It will take about a day for the water to reach Interstate 10, and two more days for it to reach Morgan City in the Cajun heartland. Morgan City’s historic downtown is protected by a 20-foot floodwall, but officials fear back-flooding as the water creeps wherever it can across the region.

Although the situation looked manageable Saturday, the Corps has warned that everyone needs to remain vigilant. The Corps has jurisdiction over a vast network of earthen levees and flood-control structures that are being pushed near to their design limits. Three Mississippi River spillways are now open to ease the flow downriver and keep the levees from being overtopped or eroded away.

“There are a lot of on-ramps of water coming into the Mississippi, and there are only a few off-ramps,” said Col. Edward Fleming, the Corps’ New Orleans District commander.

The Mississippi remains at near-record levels north to Illinois. The river will not crest at Morganza for another week, and the crest will gradually move to Baton Rouge and New Orleans.

“We still have our engineers walking the levees, look for sand boils and other weaknesses,” said Maj. Gen. Michael J. Walsh, president of the Mississippi River commission, at a news conference in Morganza before the spillway was opened.

“This is clearly going to be a marathon and not a sprint.”

Officials and residents in Baton Rouge and New Orleans, fearing floods that some officials had warned could be as destructive as Hurricane Katrina, had been eager for the opening of the spillway. The Corps did that, but gradually, starting with just one bay in a long structure that runs tangentially to a river bend.

The spillway, finished in 1954, was intended for precisely this type of situation. It had been opened only once before, during the flood of 1973. In the days ahead, more bays will be opened, and at its peak the spillway will divert about 125,000 cubic feet of water per second, less than one-tenth of the Mississippi’s anticipated peak flow. The structure is designed to release as much as 600,000 cubic feet per second.

One reason for the gradual release of water is to give wildlife in the floodplain, including black bears, a chance to find higher ground, Fleming said. The Louisiana National Guard has gone door to door warning people in the inundation area to leave, and now the floodwaters will reinforce the message.