Wappapello Lake crested Tuesday morning and Clearwater Lake is not expected to crest until Wednesday.
Officials say rainfall Wednesday could continue to set record levels.
Each lake is releasing water from both its primary and secondary spillways.
Clearwater has never topped its overflow spillway and reached more than 367.6 feet, more than a foot higher than the previous record. It is expected to crest at 568.3 feet. Clearwater controls water released into the Black River.
Wappapello reached at least 398.16 feet before it began to go down, falling short of the 400.01 record. Wappapello controls water released into the St. Francis River.
The National Weather Service is predicting up to 3 inches of rain could fall north of Poplar Bluff through Thursday morning.
Wappapello could still see a record elevation, said project manager Cindy Jackson. The lake is currently seeing a combined outflow of 22,700 cfs from its primary and secondary spillways.
Clearwater believes combined outflow from the its two spillways will not top 5,000 cfs, said project manager Randy Devenport. This is about 25 percent higher than the previous outflow record, but falls short of the 7,500 maximum the lake could have seen under earlier predictions.
Both lakes and dams are operating as intended, U.S. Army Corps of Engineer personnel say.
Both lakes have placed staff on 12-hour shifts and are monitoring instruments around the clock.
"We are currently running 24/7 operations, with engineers and our personnel on site," Devenport said, adding additional support staff have been sent from the Little Rock, Ark., district.
Wappapello has also received additional staff from the St. Louis district, Jackson said.
Water first began crossing the Clearwater overflow spillway at 1 p.m. Monday, Devenport said. The water is expected to cross a section of Highway 34 west of the project office. This part of the road was closed at noon Monday and could be damaged if strong surges are seen in the water.
Wappapello topped its secondary spillway shortly before 9 a.m. Monday. A section of Highway T below the spillway was closed around 8 a.m. and has since been significantly damaged by the force of the water.
All of the road pavement had washed away by early Tuesday morning, with a few of the under-road culverts remaining.
Jackson credits a new water control plan with helping lower the total outflow to 22,700. Outflow reached 32,000 in 2011, which was only the second time in the lake's history that the secondary spillway was used.
The new plan provides more flexibility in responding to high water events, Jackson said. It allows the lake to increase to a 10,000 cfs release from the primary spillway if a lake level of 380 is predicted, she said. Under the old plan, the lake had to be at 380 feet before increasing the primary spillway release.
The Wappapello secondary spillway has a height of 394.74.
The Clearwater secondary spillway has a height of 567 feet.
Clearwater rose more than 30 feet in a 72-hour period, Devenport said. About 9 inches of rain fell from Friday through Sunday, with 6 inches coming down in a 24-hour period.
The volume of water coming into the lake increased from an average of 46,000 cfs on Saturday to more than 100,000 cfs on Sunday. It dropped to 35,000 cfs on Monday.
Communities near both Clearwater and Wappapello have also been affected by high lake stages.
About 50 homes below Clearwater were under a voluntary evacuation Monday because of the unprecedented use of the overflow spillway. A shelter was set up at the Piedmont elementary, but no one had checked in by late Monday afternoon. Many families were staying with friends or relatives, or at local hotels, according to shelter staff.
An approximately 30-foot high berm was built on the northern edge of Greenville, near Highway 67. Two pumps are expected to be in use today to remove lake water from Wappapello, which was backing up on the highway and western edge of town.
Wayne County Emergency Management Agency Director Kent Bowman said he had not received any reports of flood damage to homes as of Monday afternoon. The county was continuing to monitor flooding potential from both Wappapello and Clearwater.