South Africa's water quality is fast deteriorating but the shrinking scientific and engineering capacity to counter this is emerging as the "real crisis" to strike the country.

This is according to Dr Anthony Turton, a senior water researcher at the Council for Scientific and Industrial Research (CSIR), who maintains that up to 50 percent of municipalities "do not even have one qualified engineer" on their staff.

Turton cites scientific research to counter the toxic cyanobacteria, also known as blue-green algae, which is found in most of SA's river and reservoir systems, according to a recent CSIR study, and can cause diarrhoea and vomiting - and even liver damage over time.

"The original work for that was done in the 1980s in massive programmes based at the CSIR," says Turton. "Those programmes generated many PhD graduates, but also did the primary science on which future management will be based.

"Those programmes are no longer in existence and this is a national crisis of note. We need to recover the bits and pieces we can and then develop new national capacity," says Turton.

He says cyanobacteria produce microcystin, a group of toxins with different chemical properties and medical manifestations.

"The worst case in Finland is 10 micrograms per litre; the worst case in the US is 60 micrograms per litre; the current South African level is 10 000 micrograms per litre with some spiking to 15 000.

"Nowhere else in the world is this happening so we cannot turn to other countries and say: 'Please help us'. We as a nation will be required to solve this problem as a nation. This is where national science councils come in. They are national assets, but the current funding models are so restrictive that their potential is being reduced and the capacity they have is being privatised."

A CSIR study released earlier this year, titled State of the Nation Report, found cyanobacterial blooms recorded in many "if not most" of river and reservoir systems - where most of SA's drinking water is obtained - because of "prevailing high levels of eutrophication caused by inadequate treatment of domestic and industrial effluents" discharged in their catchments.

While cyanobacterial poisoning is widespread among livestock, domestic animals and wildlife, there are no known human fatalities, says the report. "The deemed health risk to humans is via long-term chronic exposure to low levels of cyanotoxins in water used for drinking and domestic uses because it's estimated only 21 percent of households have access to piped water inside their homes."

Conventional water treatment processes are "ineffective" at reducing cyanobacterial toxins, it adds.

Turton says climate change is already having an impact. "Increased ambient temperatures in dam water is changing the population dynamics of the cyanobacteria that produce the microcystins and this is happening here and now. It's already on us … we need to listen to our own South African scientists and empower them to do their work. So this is the real crisis."

Last week, Minister of Water Affairs and Forestry Lindiwe Hendricks, revealed at the municipal water indaba that 60 percent of municipal wastewater treatment plants are operating below standard. River pollution, too, is at an "unacceptable" level.

"There are very real skills shortages in our country," Hendricks stated "These are not only skills at the higher level of university trained engineers and scientists but at all levels throughout the water and sanitation value chain."

Her department has now proposed a new blue and green drop certification initiative, which will award those municipalities compliant with good drinking water and wastewater standards with blue and green drop status certificates, meaning they can market their safe drinking water to citizens and tourists.

Those failing to comply will receive red drop status and would be publicly "named and shamed".