Zandvlei has been closed since Tuesday May 25 because of high levels of E coli.
The most recent samples taken in Zandvlei show the water quality is still not good enough to open it, says Zandvlei Nature Reserve manager Kyran Wright.
Meanwhile Marina da Gama residents have welcomed news that a previously unidentified sewage leak into the vlei has been located and stopped.
Mr Wright said further sampling would be arranged for the coming week to see if cleaning up that spill would have led to any significant improvement.
Xanthea Limberg, mayoral committee member for water and waste, said the City has been investigating the catchment for other possible sources of pollution.
"An overflowing manhole has been discovered next to the river. The cover and frame have been stolen," she said.
"This manhole is well hidden between the reeds and does not appear on the City’s record drawings. It has been repaired to a higher level, to avoid possible pollution of the river in the future," she said.
Ms Limberg said the City’s water and sanitation department suspected that the manhole could have been running intermittently over the past month.
She added that the Keyser River pump station had failed on Tuesday July 27.
"The overflow started at approximately 10am and was resolved at 11pm on the same day. Currently, one pump is operational at the pump station and it is coping with the flow," she said.
It was unclear at this point whether the pump station failure and the overflowing manhole could account for all the high readings seen over the past two months, but they had obviously contributed, she said.
"The City has been conducting regular water tests to monitor the water quality and continues to investigate possible undiscovered pollution sources based on these results," she said.
A lot of the pollution in the catchment was linked to abuse/misuse of the sewer system, vandalism, illegal connections, and other factors, she said.
"The City will continue with efforts to raise awareness about the causes and effects of sewer blockages, as the majority of infrastructure failures are avoidable," she said.
It was taking a long time to get the message across to the public that sewer overflows were a direct result of flushing the wrong things, she said.
The City’s commitment to becoming a water sensitive city by 2040 would take time, she said, “as our urban environment treads heavily on the natural environment”.
Mr Wright said sediment-removal work started in the lower reaches of the vlei last year would continue in the week ahead and throughout the rest of the month.
"The purpose of these efforts is to decongest the lower reaches of the vlei, leading to improved catchment flushing and fish migration. During this time, sand will be stockpiled in certain areas, which will be off limits to members of the public due to safety concerns. Please also note that the collection of disturbed sand prawns is not permitted," he said.
Marina da Gama residents Mike Ryder and Gregory Higgins, while pleased that a previously unidentified source of pollution has been fixed, are still calling for the City's E coli readings to be released publicly.
Mr Higgins said it is insulting to be told that the readings were complex and required certain contextual and technical knowledge to be interpreted, and Mr Ryder said he was willing to take his chances in interpreting the information, rather than having nothing to work with.
Mr Wright said he would request the information from the relevant department but he needed permission to share it.