Jim Willis of Mount Pleasant and his wife Debbie were traveling on the Atlantic Intracoastal Waterway when their vessel struck a shoal near Breach Inlet.

The impact caused her to fall backward and hit her head. In the emergency room, doctors determined she had a fractured vertebrae, a concussion and a broken rib. Nine staples were needed to repair a gash in her scalp. She spent two nights in the hospital.

"Her mobility probably won't be 100 percent," Willis said. "She can't rotate her head from left to right as much as she used to."

Since the accident in October, the couple has stayed away from the inlet between Isle of Palms and Sullivan's Island in their waterway travels, although they would probably go back there at high tide. The accident happened about two hours after low tide, he said.

They were traveling in the center of the channel in a 44-foot trawler drawing 3 feet, 10 inches of water. The channel is supposed to be maintained to a depth of 12 feet at mean low tide.

For decades, the waterway has been a key transportation route for barges and pleasure boaters from Virginia to Florida. But in recent years, it has fallen into disrepair as federal funds for dredging have dried up. In South Carolina, the problem has accelerated to create worries about the risk of traveling the ribbon of water designed to provide safe inland passage sheltered from the dangers of the ocean.

In Charleston County, the shallow waters at McClellanville and Breach Inlet are major concerns. County Councilman Dickie Schweers is leading an effort to increase funding for waterway channel dredging at those locations. On Thursday, he received the endorsement of the council, which voted to spend $500,000 over two years if the state and federal governments provide "substantial" matching funds.

In some places of the waterway, the "low-tide effect" is like suddenly narrowing the Arthur Ravenel Jr. Bridge from eight lanes to two lanes, said Anthony Noury, owner of Sea Tow in Mount Pleasant.

The conditions drive boaters to try the open ocean as an alternative route. "It can be nice, but it can also go bad on you really quickly. Then they run into trouble," he said.

Boats that stay in the waterway may be damaged by the shallow channel. Two large recreational vessels were recently towed to the City Marina in Charleston with broken drive shafts caused by hitting bottom at Breach Inlet.

"It's not unusual," said Robert Freeman, managing partner of the City Marina Co.

"These are some of the wealthiest tourists who come here. When they have a bad experience, they're not going to come back," he said.

The shrimping fleet based in McClellanville is hobbled by waterway conditions, said Mayor Rutledge Leland.

About half of the two dozen boats require deeper water. They are limited to moving around at high tide on the Jeremy Creek portion of the waterway, he said.

"It's mud at low tide. It's a huge problem. All we are doing is taking little steps," Leland said.

One of those steps was taken Thursday night when Charleston County Council approved spending seed money on dredging the waterway if the state and federal government were willing to shoulder the bulk of the cost, estimated to be in the millions.

Dredging to required depths at Jeremy Creek would cost more than $3 million. It would take about $2 million to fix the problem at Breach Inlet, according to the Army Corps of Engineers.

In Charleston County, the waterway moved 170 tons of commercial freight in 2012, according to the latest available figures. It is considered a marine highway much like what Interstate 95 is to cars, said Brad Pickel, chief executive officer of the Atlantic Intracoastal Waterway Association, which is based in Beaufort.

The Corps of Engineers, which handles waterway maintenance, has been hamstrung by a shortage of money. In this area, the waterway was last dredged in 2010 using funds from the American Recovery and Reinvestment Act, said David Warren, civil works project manager for the Corps Charleston District.

The president's budget, which has yet to receive congressional approval, would provide $500,000 for local waterway maintenance beginning Oct. 1. Those funds could be used to design dredge projects so they are "shovel-ready" when more funds become available, Warren said.

"I'm almost positive we are going to get that money. I'll present a plan to our leadership as to how I would like to use it," Warren said.

Waterway maintenance also includes mosquito abatement, he said.

At its website, the Corps Charleston District has waterway navigation charts based on channel data gathered last year.

"It's much more up-to-date than NOAA (maps)," Warren said.

Commercial waterway users are also calling for channel dredging.

Shoaling limits the steel tonnage that Stevens Towing of Yonge's Island can move on the waterway, said Bos Smith, the company's South Carolina operations manager.

Some 25 percent less product from Nucor Steel Berkeley is shipped on barges because of the shallow channel, he said.

The capacity of one barge equals 30 jumbo rail cars or 120 tractor-trailers, officials said.

"It's an industrial highway," he said.

At McClellanville, the problem with the inland waterway is particularly bad. "It has been nicknamed 'Mudville,' " Smith said.

The situation is a "classic Catch-22" because funding for dredging to 12 feet is based on tons of cargo moved. But barge traffic is limited because of shoaling, he said.

There have been navigation issues in other sections of the waterway.

South Carolina ranks last when it comes to federal funding for intracoastal dredging, Pickel said.

Some states, such as Florida and North Carolina, have dedicated funding for waterway maintenance. The Florida Inland Navigation District collects about $20 million annually to pay for waterway maintenance in 12 counties, said Mark Crosley, the district executive director.

About half of the organization's budget goes to the Corps of Engineers for dredging. The rest is used as matching funds for communities that are building waterfront improvements such as parks, piers and boat ramps.

North Carolina funds waterway maintenance through boater registration fees and the gas tax.

A well-kept waterway has billions of dollars in economic benefit, Pickel said.

Willis agreed.

"The waterways are a huge source of revenue and jobs. It would seem that the state, city and county would all want to support it," he said.