The victim was 33-year old Aron Thomas, an employee of the office. The shooting happened shortly before 7 a.m.
Kingston Police arrested a co-worker, 53-year old David Reese of Gilboa, N.Y., and have charged him with second-degree murder.
"Both men were expected to work today. Both men logged in which was their usual custom, and this incident happened pretty shortly after the second individual logged in," said District Attorney D. Holley Carnright.
A handgun was found in the facility and is believed to be the weapon used in the shooting.
For now, investigators will not reveal a possible motive.
"We are not releasing that information right now," said Carnright. "We are developing information. It's an ongoing investigation."
In a written statement, DEP Commissioner Carter Strickland said: "We are shocked and saddened by the senseless act of violence. The thoughts and prayers of all DEP employees are with the victim's family and loved ones."
The DEP says it's providing grief counseling to other workers.
The DEP offices in downtown Kingston house employees who oversee the city's upstate reservoirs.