Captain Joseph F. Maloney Jr. of the Boston Harbor Pilot Association was making coffee on his boat early Tuesday morning when he heard the distress call come in: A tugboat with three men aboard was rapidly sinking at the mouth of the Boston Harbor.

“I know the captain, and I could hear the desperation in his voice. He said, ‘Joe, you need to get here — now,’’’ said Maloney in a telephone interview.

The 51-foot tugboat Emily Anne sank at the end of the North Channel, six miles east of Deer Island, just before sunrise, in 44 feet of water, said Petty Officer Cynthia Oldham, a spokeswoman for the Coast Guard.

Already on the water — “we’re always on the water,’’ according to Maloney — and about a half-mile from the sinking vessel, Maloney and co-captain Shawn Kelly raced to the scene.

By the time they had arrived, the boat was gone, he said, but its captain, Doug Richman, and two crew members were floating in the cold waters.

Maloney said he and Kelly pulled the men from the water and got them back to land. They were in the water for no more than five minutes before they were rescued. One was on a life raft, and the other two were in the water.

The Coast Guard had dispatched crews to help with the rescue, but the men had already been pulled from the water by the time they arrived, Oldham said.

The men were evaluated by EMTs and were in good condition, said Oldham.

The Coast Guard said it was investigating the cause of the sinking.

“It’s unknown at this time. We just know there was massive flooding in their engine room,’’ said Petty Officer Dean Drake. Crew members “were trying to keep up with the flooding with their water pumps, and they weren’t able to keep up.’’

Captains from the pilot association navigate large ships in and out of the harbor and are usually not part of rescues. Maloney said he was calm during the “crisis,’’ but once he reached land, the reality of the moment hit.

“I’m just feeling the adrenaline now. I’m getting that big adrenaline dump,’’ said Maloney. “We were very lucky everything worked out.’’

Globe correspondent Lauren Fox contributed to this report. Steve Annear can be reached at steve.annear@globe.com.