A serious water quality issue that was about to "burst into the boardrooms of large corporations and the corridors of government" was acid mine drainage from coal and gold mining, according to CSIR scientist Anthony Turton.
Another issue was the high levels of eutrophication in the country's water - an increase in chemical nutrients, often from fertilisers, that leads to plant bloom and decay, polluting the water and removing the oxygen.
South Africa, a water-stressed country, had levels of eutrophication "almost unpre-cedented globally", Turton said.
These were some points Turton raised in the keynote address, A Clean South Africa, that the CSIR executive prevented him from giving on Tuesday at a CSIR conference entitled Science Real and Relevant.
Turton said South African dams also had one of the highest loads of microcystins in the world.
These are toxins produced by blue-green algae, which cause liver damage and can be fatal. No serious study has been done on this problem since the mid-1980s.
Other problems were the build-up of endocrine disrupting chemicals and partially metabolised medication in our water. Because of the high rate of HIV and Aids, there would be an increasing use of anti-retro-virals. These passed through the body in a partly meta-bolised form, eventually into our rivers.
These chemicals would begin to enter the South African population either through drinking water or through produce irrigated with contaminated water.
"We need to develop the science to understand this better, because nowhere else in the world is there a coincidence of loss of dilution (of chemicals in water because of water scarsity) and high levels of ARV use as in this country," he said.
As a result of more than a century of largely unregulated gold mining, South Africa had a legacy of heavy metal and radionuclide contamination of rivers, but no study had been done to determine the impact on people exposed to them. Large parts of Soweto and the East and West Rand were built on contaminated land.
A theme in Turton's paper was that it would take an enormous amount of technical and scientific ingenuity to solve South Africa's water quality problems, but that there was a shortage of scientific, engineering and technical capacity in the country.
The CSIR needed a sustained source of public funding to produce the scientific capacity to address these problems. Without it, the CSIR ran the risk of being "hijacked by private interests, which have no wish to open up this complex legacy issue", Turton wrote.
"Do we wish to avert the water crisis... or deal with it after it has been thrust upon us like the electricity crisis?" he wrote.
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