Mr. Evans, who works in the city agency’s Bureau of Engineering Design and Construction, has been suspended pending an investigation, agency officials said. He was set to be arraigned on Thursday night. Mr. Nieves and Mr. Hannibal were given desk appearance tickets and will appear in court later; attempts to reach them by phone and Facebook on Thursday were unsuccessful.

Police officials said there was not much more that could be done to further protect the sewage system from intruders. “The reality is we cannot be everywhere protecting everything from everybody,” Commissioner Bratton said.

“What happened here last night is what we ask people to do: See something, say something,” he added. “Somebody saw them, it is an out of the ordinary action, and we responded.”

Officials said there was a reason the sewer system was closed to the public. “Entering a sewer without proper authorization and training is illegal, incredibly irresponsible and dangerous,” Chris Gilbride, a spokesman for the Department of Environmental Protection, said in a statement.

The sewer system is not exactly the network of cavernous corridors as it is sometimes depicted in popular culture, officials said. Instead it can be confining in places, filled with overpowering fumes, and tunnels can rapidly fill during heavy rain.

Manholes can be difficult to penetrate. The covers can weigh as much as 195 pounds and require a crowbar or a similar tool to open.

The limited access seems only to feed into the mystique.

“They’re dark and mysterious and off-limits,” said Michael Miscione, the Manhattan borough historian. “Your imagination runs wild.”