The danger is that the Umbeluzi river may inundate the water treatment station, forcing it to halt operations.
Already, the access road from Maputo to the treatment station has been cut by the rising waters.
The authorities are urging Maputo residents to economise in their use of water until the situation is normalised.
Some parts of the city already lack drinking water following weekend rains that broke water mains.
The education ministry has closed schools in Maputo and Matola (and in parts of the flood-stricken district of Chibabava, in the central province of Sofala) until 14 February.
Its spokesman, Zefanias Muhate, said the decision was taken because so many Maputo and Matola residents have lost their homes and property.
"This situation, plus the fact that many access roads have been damaged by the mudslides, means that neither pupils nor teachers are able to travel", he said.
Furthermore, several schools are being used as temporary shelters for the thousands of people displaced from their homes by the floods.
Maputo provincial governor Soares Nhaca has warned that the dam reservoirs in the province are virtually full, and this will force the authorities to increase the discharges from the Corumana and Pequenos Libombos dams.
The most serious threat is of a major flood on the Incomati river. At Ressano Garcia, where the river enters Mozambique from South Africa, the flow of the Incomati increased dramatically between Sunday evening and Monday morning, according to the Southern Regional Water Board.
The height of the river rose from 3.63 to 6.92 metres. Flood alert level at Ressano Garcia is five metres.
Reports from South Africa say the level of the Incomati will continue to rise.
Meanwhile, the meteorology services said from Friday to Monday 454.5 millimetres of rain fell on Maputo.
Of this total, 328.3 millimetres fell in less than 24 hours.
Persistent but less intense rainfall have been forecast until Thursday.
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