People stand outside a house surrounded by floodwater in the aftermath of Hurricane Irma in Callahan, Fla., outside Jacksonville. (Jabin Botsford/The Washington Post)

While the rest of Florida began picking itself up after Hurricane Irma, this city in the far northeastern corner of the state was still experiencing serious flooding and was bracing for more inundation to come.

Some floodwaters from the massive tropical storm were expected here, but the scale of the unfolding disaster took Jacksonville and nearby towns by surprise. Driven by tidal flow, an already saturated inland waterway system and Irma’s powerful winds and rains, the swollen and fast-rushing St. Johns River crashed over sea walls and sandbags and left much of the area underwater.

Officials called the flooding “epic” and “historic,” with the river through this city of nearly 900,000 hitting levels not seen since 1846 — a year after Florida became a state. On Tuesday the city started to recover, but meteorologists warned that some flooding is likely to return as storm-generated waters rush south from the Carolinas toward the Atlantic Ocean.

The St. Johns — 315 miles long and three miles wide at points — is expected to continue threatening communities in northeast Florida because the huge volumes of water the river is holding have no place to go, according to Angie Enyedi, an incident meteorologist with the National Weather Service.

“The water will subside very gradually within the St. Johns River basin. The water is trapped in the St. Johns, and essentially ‘sloshes’ north to south within the river with each high tide,” Enyedi wrote in a memo about the disaster. “Major river flooding will continue for many more tide cycles.”

Homes in the flooded San Marco neighborhood of Jacksonville. (Jabin Botsford/The Washington Post)

Hundreds of residents had to be rescued from the rising waters in Jacksonville and nearby communities after they chose not to heed pleas from local and state officials to flee the area ahead of Irma. Millions of Floridians had headed north to escape Irma’s potential path after officials warned that the once-powerful storm could cause catastrophic damage to several Florida cities.

“We hope the 356 people who had their lives saved yesterday will take evacuation orders more seriously in the future,” the Jacksonville sheriff’s office tweeted Tuesday.

The evacuation order was lifted Tuesday. Business owners returned to riverfront shops and restaurants to find sea grass, tree limbs and an inch of mud covering streets and some sidewalks. By midday, the mud started to give off a strong odor as it baked in the hot sun.

At Jacksonville Landing, a marketplace on the river near EverBank Field, home to the Jacksonville Jaguars, the only business open was a Hooters restaurant that had closed Friday night ahead of the storm.

“We came in, cleaned up and got it open,” said Hooters regional manager Cindy Ingram.

A scrap yard full of vehicles is seen covered by floodwater in the aftermath of Hurricane Irma in Callahan, Fla. (Jabin Botsford/The Washington Post)

In Clay County, about 40 miles south of Jacksonville, the Black Creek was still flooding neighborhoods and roads. The creek crested Tuesday morning at 28.5 feet “and likely won’t begin receding until Friday,” according to county spokeswoman Kimberly Morgan.

More than 37,500 people were without power in Clay County, and Morgan said residents should be prepared to go without power there for a week or longer.

Kimberly Robinson, public information officer for the Green Cove Springs Police Department, said a nor’easter that hit the area shortly before Irma came through made matters worse. “All that water just had nowhere to go,” Robinson said.

The area was hit by Hurricane Matthew last year, but Robinson said the experience was very different. “Matthew came in and water came up, then it went back down,” she said. “We’ve never experienced anything like this.”

Homes are left surrounded by floodwater in the aftermath of Hurricane Irma in St. Augustine. (Jabin Botsford/The Washington Post)

With Green Cove Springs virtually shut down because of power outages, residents were cleaning up and also taking a break. William Saylor, a service manager at a car dealership, went to the town’s riverfront park Tuesday morning. The park’s gazebo, normally about 20 yards from the shore of the St. Johns River, was now at water’s edge. Saylor took out his fishing rod, put a plastic worm on it, and hooked a three-pound largemouth bass within seconds.

“The water pushed all the bait fish too far out, so the bass are coming up here looking for food,” he said. “They’re hungry.”

Saylor released the fish back into the water at a spot where children usually play in the grass. “It’s kind of crazy to think that you could fish here,” he said. “This water should be 30 yards out.”

On Tuesday, life in the coastal city of St. Augustine — the oldest permanent city in America, founded on Sept. 8, 1565 — was probably more like it was 450 years ago than it should be today. The city was still without power. Trolley tours in the historic downtown were shut down.

Restaurants were closed. Workers were suctioning water out of the lower floors of the Florida School for the Deaf and Blind, and business owners were mopping up floors and picking up tree limbs.

“We sandbagged, we caulked, we boarded up, we taped plastic, and the water still found a way in,” said Adam Amoia, owner of Romeo’s Cafe on Cathedral Place, just up the road from the historic Castillo de San Marco fortress. “When we walked in here, it was like the beach was dumped on the floor.”

Amoia had to walk three miles to see the damage Irma wrought on his business on Monday, because all roads leading to the town were blocked. He and his crew started mopping out the water and drying the floors at dawn Tuesday.

They were working in the dark, and in the heat. He’s confident that Romeo’s — home of the “Bubble Waffle” ice cream cone — will be up and running soon, but he is getting weary of hurricanes.

“This will be our third grand opening,” Amoia said. “We opened almost two years ago, reopened after Matthew, and now we’ll have another reopening after Irma. I’m ready to just stay open for good.”

Homes in historic St. Augustine after flooding from Hurricane Irma. (Jabin Botsford/The Washington Post)