The Syrian army entered the area in the Wadi Barada valley as part of an agreement with rebels that have been fighting to hold it, Reuters reported.
The deal will include the evacuation of insurgents from the area.
The Syrian capital gets most of the water from springs in the Wadi Barada valley. Water supplies were drastically reduced in late December. The UN fears the water network could have been damaged by fighting or sabotage by armed opposition groups.
UN's humanitarian coordinator Jan Egeland has said that 5.5 million people had their water supplies cut or minimized after supply from the Wadi Barada spring was disrupted.