An abandoned water tunnel deep below the Charleston peninsula has sent a hiccup into the City Market flood control project.

Engineers say the old tunnel is potentially filled with dangerous amounts of water and, if breached, could put crews at risk of drowning dozens of feet below the surface where they are working on drainage tunnels.

To avoid the problem area, workers now will have to dig down 140 feet at the pump station behind the federal Customs House, instead of the previous target of 80 feet.

“Our tunnel is too close to the ‘void’ space,” Charleston Public Works Director Laura Cabiness said.

“If the soil between the new tunnel and the abandoned tunnel was breached,” she said, “the new tunnel would be flooded along with anyone and anything in the tunnel at the time.”

The shift to a greater depth means the cost of the project will increase by about $2.7 million to cover the expenses of re-routing and pouring more concrete. It also means about 206 additional workdays will be added.

The issue centers on a long-abandoned Charleston Water System line buried deep below Concord Street. It is in the same area where Charleston officials plan to install a new deep-ground line that, when completed, will help direct tens of thousands of gallons out of the flood-prone Market and into Charleston Harbor.

Barry Newton, manager of the Market, said that with the problem identified, there’s not much that can be done until the lines are corrected.

“Anytime you’re digging underground in Charleston, you’re going to find things,” he said Tuesday.

The bigger issue, Newton said, is how the delay might affect Market business later on, since additional construction will be needed to sink drainage shafts around the Market to aid in the out-flow of water.

When completed, this current phase of the city’s flood-control efforts will add at least a 40,000-gallon-per-minute drainage capacity for the Market. By 2020, Charleston will have spent more than $250 million on citywide flood control, officials estimate.

Reach Schuyler Kropf at 937-5551.