Some residents say they have not received water in their localities for more than one week, Radio Bakhita reports.
Fatnah Khamis, a resident in Malakia says she now pays 60 South Sudanese Pounds per water drum.
Previously, she used to buy water at 30 South Sudanese Pounds.
Khamis says even the water sold expensively is dirty.
Gaishubai, the Acting Managing Director of SDI water purifying company says his company has closed down one month ago due to difficulties in acquiring fuel for running the business.
Meanwhile, the Juba City Council Deputy Mayor, Ater Ayiel Wol attributes the shortage of water due to depreciating South Sudanese Pounds against the US Dollars.
The water shortage has even hit Juba suburbs of Gudele and Kator.
Efforts to reach the union of water suppliers and Urban Water Corporation for comments were unsuccessful.