Authorities are evacuating the Saline County town of DeWitt and all or part of the Jefferson County towns of Fairbury and Endicott.
In Fairbury, everything west of the railroad tracks is being evacuated because of floodwater, said Nebraska Emergency Management spokeswoman Jodi Fawl.
The Saline County Sheriff's Office, Nebraska State Patrol and area rescue departments are taking people to a shelter at Tri-County High School south of town.
In Lincoln, manufacturer Lincoln Industries at 600 W. E St. was being evacuated just before noon and the plant sent about 400 workers home for the day.
Startling photos showing the Lancaster Event Center surrounded by floodwater, and water covering the field at Haymarket Park showed the extent of Wednesday night storms in Lincoln.
City police and firefighters responded to about 90 incidents Wednesday night and Thursday morning, primarily motorists who needed help because their vehicles flooded and they needed help getting to higher ground, Public Safety Director Tom Casady said at a Thursday morning news conference.
"Salt Creek is running about as full as I’ve ever seen it," he said.
The creek exceeded its capacity south of the city, and water is standing behind the levee in a few spots, authorities said.
“We do have a sand boil on the east side of Salt Creek levee around J Street with quite a bit of water in the South Bottoms, north of the tracks, up to O Street," said Casady.
South of town, he said, gauge readings on the Haines Branch were steady and falling so Salt Creek isn't expected to rise much higher.
"A decade ago we would have had some major urban flooding with a rain like this," Casady said. "The Antelope Valley project spared us from that."
The $246 million flood control and neighborhood revitalization project was completed in 2012, and Antelope Creek stayed within the channel after the rain, he said.
The city's creek system has been engineered for 100-year floods or larger, but storm sewers were built for 5- and 10-year flood events, city officials said.
The situation had stabilized by mid-morning, said city Public Works Director Miki Esposito, who had this plea for motorists: “Don’t drive beyond the barricades."
“What we need is for people to turn around and not drive though those places, she said. “What they don’t see is that we are losing a lot of manhole covers and it presents quite a hazard to drivers. Turn around and find a new route."
Lancaster County Engineer Pam Dingman noted that more rain -- and there's a chance for more through Monday -- could mean more flooding.
"The ground is very saturated, so there is the potential for the perfect storm," she said.
People can report problems in Lincoln at 402-441-7701.
The Lincoln Airport reported 6.65 inches of rain since Wednesday morning, and even higher rainfall totals are being reported from surrounding areas including more than 10 inches in Swanton, 9 near Wilber and 8 at Western.
Earlier Thursday, Swanton officials were working to rescue people from two homes surrounded by nearly 3 feet of floodwater.
Near Lincoln, flooding closed Saltillo Road between 14th and 27th streets, as well as South 14th and 27th streets in that area. The road through Holmes Lake, the ballfields and significant portions of the golf course were under water as was Sherman Field on South Street.
Along Salt Creek, officials said the flooding extends from Roca to the south all the way to Greenwood.
The creek was 6.5 feet over flood stage Thursday morning in Lincoln and at record flood stage near Greenwood. Flood warnings were also up for the Big Blue south of Crete, the Little Blue near Fairbury and Turkey Creek near Wilber.
Thursday morning, drivers were unable to reach U.S. 77 from Warlick Boulevard, Old Cheney Road and Pioneers Boulevard. Law enforcement also reported part of the road near U.S 77 and Saltillo had buckled under stress from floodwater.
Several highways are also closed, including U.S. 77 near the Crete interchange, U.S. 81 near Hebron, U.S. 136 near Ruskin, Nebraska 63 north of Alvo Road, Nebraska 103 between Crete and Wilber and Nebraska 15 north of Fairbury.
Flooding also closed the Waverly interchange on Interstate 80 as water covered U.S. 6 in the area, but U.S. 6 was back open from 84th Street to the interstate by mid-morning.
Rail lines are closed in some areas due to the flooding, and several propane tanks had come unattached and were floating near tracks in the South Bottoms. Authorities said late Thursday morning the tanks presented no danger.
In Fairbury and DeWitt, Black Hills Energy technicians are working with emergency officials to shut off natural gas temporarily to avoid the risk of leaks that can happen when equipment or appliances are submerged and pilot lights are extinguished.
If you smell natural gas, get out and call Black Hills Energy at 800-694-8989 on a cellphone or a neighbor’s phone. Do not use the phone inside or turn any lights on or off when leaving. A spark could ignite leaking gas.