Despite the heavy rains, water levels in various dams have shown no progress.
The Department of Water and Sanitation said the rains in Gauteng, parts of Mpumalanga and Limpopo have had little impact on the country's water situation, with dam levels still dropping by one percent weekly.
National dam levels have dropped from 57.6% to 56.1% this week.
Department spokesperson Sputnik Ratau said hydrologists attributed this state of affairs to the heavy rains falling in regions that have little or no catchment areas.
The week-long rains caused widespread flooding in Gauteng, with several motorists and residents in Centurion and Mamelodi, Pretoria, left stranded as a result.
"Meanwhile, Joburg and Tshwane metros are keeping their water restrictions in place while they are assessing the cumulative impact of the heavy rains in the two cities.
"The latest report that was issued by the department suggests the heavy rains only had an impact on smaller dams in regions that did not have sufficient catchment areas to harness rainwater," said Ratau.
An overview report by the department shows that overall, at national level, dams are still at a lower average level and still falling slightly despite a few increases.
However, the good rains in Gauteng and Mpumalanga accounted for increases in some related dams; while dams in Limpopo and the North West showed modest improvement.
"Dams in the Eastern Cape, KwaZulu-Natal, Western Cape and Lesotho continued their modest decreases, while significant drops were recorded in the Free State and Western Cape. The Western Cape has entered its dry summer hydrological season until May next year. Dams in Mpumalanga, upper Limpopo and the northern Free State will benefit from the Gauteng run-off over the next week," according to the report.
"The weekly report painted a gloomy picture of the water situation in the Eastern Cape, where vast parts of the region are experiencing extremely dry conditions to a complete drought. Regions under stress are Butterworth, towns falling under the Chris Hani District Municipality and eight others under the jurisdiction of Joe Gqabi," Ratau said.
He added the Xilinca Dam and smaller weirs that provided water to Butterworth and surrounding areas in the Eastern Cape were empty.
The department is continuing to help alleviate the impact of this misfortune in the stressed regions of the province, including funding in the region of R248m already spent.
Two weeks ago, Water and Sanitation Minister Lindiwe Sisulu met with the mayor of Butterworth and other principals to discuss ways of intervening in a town where the local dam has run dry completely.
Meanwhile, the situation remains desperate in the Mopani region of Limpopo, where the Tzaneen and Middel-Letaba dams dropped to 4.8% and 2.7%, respectively. Given the situation in the region, it is another area of concern for the department and Sisulu.
She has reiterated her appeal to shack dwellers and those who live below the flood line to relocate immediately to higher ground and safer areas to avoid being hit by floods.
Last month, the eThekwini metro embarked on a drive to warn people, who have their structures next to rivers such as Isipingo River in Durban, to move in anticipation of the heavy rains that might result in localised flooding.
The warning has now been extended to everyone who live below the flood line along the coastal belt to relocate immediately.