Fuel shortages and sporadic fighting mean water must be carried from the pipeline sending water to millions of people in Tripoli, Benghazi and Sirte.
UNICEF said it secured around 1.3 million gallons of water from Libya's neighbors, which is sent via truck to the Libyan capital.
Around 23,000 bottles of emergency water supplies arrived in Libya during the weekend and the International Committee of the Red Cross was stepping in to help with water trucked in from Tunisia.
"UNICEF is responding to the immediate needs," said UNICEF Libya chief Christian Balslev-Olesen in a statement. "But we remain extremely concerned about the situation should the water flow to Tripoli stop in the coming days. This could turn into an unprecedented health epidemic."
Power cuts and fuel shortages means about 6 million people in Libya are running out of water.