The Mississippi River fell back below flood stage in Vicksburg Thursday night, signaling the lowest mark on the river since May 1 and the start of an arduous repair of the flood protection system on mainline levees and banks in the lower river system.

Stages in the city this morning stood at 42.5 feet, down 1.1 feet. Levees and control structures along the river from Rosedale, Miss., to Lake St. John in east-central Louisiana passed the river’s sternest test in decades — but left behind 11 “hotspots” where damage has been confirmed, top U.S. Army Corps of Engineers officials said Thursday during a tour of the river on the MV William James.

“We knew that we were going to be testing it at a level we’d never, ever seen before,” said Col. George T. Shepard Jr., deputy commander of the Mississippi Valley Division. “This was the epic flood. The system took a beating, but it performed as designed.”

The river crested 14.1 feet above flood stage in Vicksburg on May 19, at 57.1 feet, topping the 1927 mark by nearly a foot. A new high-mark also was set at Natchez, where the river crested the same day at 61.9 feet. Peak daily flows topped 1927 levels at Vicksburg, where more than 2.2 million cubic feet of water was measured, and at Arkansas City, Greenville and Natchez. Rainfall in the last two weeks of April in the Ohio River Valley was between 600 percent and 1,000 percent above normal, and fell below control structures — a combination of factors that helped cause the record floods on the Lower Mississippi, Shepard said.

No additional money for the Mississippi River and Tributaries Project, the process in place since 1928 for controlling floods on the Lower Mississippi, means some “tough decisions” lay ahead in the coming months on which problem areas are funded, Shepard said.

“As we all know, resources are constrained in pretty much anything you do,” Shepard said. “All the districts will be bringing their projects to us, and we’ll start racking and stacking them.”

The Corps expects about $210 million from Congress in fiscal 2012 for the main funding source for levee maintenance and bank stabilization, $100 million less than 2010. The Corps’ overall budget expects 6 percent less money than this year and 15 percent less than 2010. Lists offered by each district are certain to be whittled down to fit money pools, Shepard said. Most pressing needs in the Corps’ Vicksburg District involve building sand berms, relief wells or both at the 11 most vulnerable locations on the mainline and backwater levee systems. Three nearest to Vicksburg are at Buck Chute, just west of Eagle Lake, at Lake Albermarle and at the Yazoo Backwater Levee. The Corps rushed to complete a 2-acre berm at Buck Chute in early May. A more permanent fix involves a shorter berm but with multiple relief wells to avoid raising lake levels and threatening homes within feet of the water’s edge in the resort community. A similar plan is in the works farther north at Albemarle, where a slide and several boils broke out days before the river’s crest in Vicksburg. Low spots need to be filled on the 28-mile backwater levee. In addition, four miles of polyvinyl mat laid in case water had overtopped the structure will be removed and possibly recycled. Enough funding is in place to award a contract to address Buck Chute by late September or early October, said Col. Jeffrey Eckstein, commander of the Vicksburg District, stressing analysis of the levee system will be done across district lines.

“It’s a systemwide approach,” Eckstein said. “We’ll look at our available funding.”

Eight other areas needing berms and/or relief wells include one in northwest Bolivar County, two spots north and south of Greenville in Washington County, near Lake Chicot in southeast Arkansas, at Henderson in East Carroll Parish, La., near Lake Bruin in Tensas Parish, La., and at Lake St. John in Concordia Parish, La. Work to raise part of the levee in Vidalia, La., by 4 feet was halted by the flood, but is expected to continue, taking three to five years.