"Once all of this is out we will have to get in there, take out the remains of the broken pumps, which have been vandalised, and install new ones," said Staff Sgt Mandla Dickson at the Sebokeng water treatment plant.
"What we are doing now is exactly what we did while on peacekeeping missions in the Democratic Republic of Congo. The damage that we encountered there, which was from years of war and neglect, is equivalent to what we are finding here."
The soldiers have been deployed to 44 collapsed facilities. They are supported by armoured vehicles. Last month thieves killed two security guards at the Meyerton water treatment facility.
"These facilities are now military zones," said Mahapa, whose 200 troops will soon to be reinforced by 300 more. "We just pray we do not have to shoot anyone."
He said the army was working with the department of water and sanitation, municipal officials and engineers.
Makhura told the Sunday Times that rebuilding and repairing 44 sewage pump stations that were leaking into the Vaal River needed to be done immediately.
"If Emfuleni's issues are not addressed the disaster will impact beyond Gauteng."
Mike Muller, a former water affairs director-general who helped write the water security plan, said the research showed that though sewage pollution was increasing, R15bn was being budgeted to address acid mine drainage, "which is not the greatest pollutant".
WATCH | Soldiers try to alleviate the flow of raw sewage into the Vaal river