Botulism has broken out among the wild birds at Century City's Blouvlei wetland, home to several rare waterfowl species, where about 130 birds have died.
The contaminated bird carcasses are being burnt on site in a makeshift incinerator to prevent the disease, which cannot infect humans, from spreading.
The botulism bacterium blocks the bird's nerve impulses and paralysis sets in. Infected birds cannot fly or walk and ultimately it affects their respiratory muscles and they suffocate.
Century City environment officer Dries Weyers said on Monday that the disease had broken out just over two weeks ago.
Weyers said: "On the first day we found 80 dead birds, the second day 25 and the third day it was down to four. On Friday there were none and this morning there were three from over the weekend, so I think the outbreak has been contained.
"But we're patrolling the whole area daily - all the canals and vacant land, too. It takes us about three to four hours a day. We're going to have to keep on monitoring it for the next few months."
A member of the Tygerberg Bird Club was the first to spot the dead birds two weeks ago and alerted city scientific services manager and fellow club member Dirk van Driel, who has so far been unable to establish the source of the botulism.
Van Driel said on Monday: "The botulism bacterium sits in the soil and can stay dormant for a long time. It needs animal protein to become virulent.
"One dead carcass on contaminated soil can spark off an epidemic. We have to burn the dead birds to kill the bacteria. If we don't do that, there won't be any birds left."
The botulism has affected mainly Sacred Ibises and some coots. Ibises scavenge by pecking on rotting carcasses and could contract botulism from the carcass itself or from eating maggots in the carcass.
The infected birds then contaminate the water with their faeces so that ducks, geese and other waterfowl become infected.
Van Driel said the botulism bacteria could breed in places like poultry farms, if dead chickens and eggs were thrown out with the chicken manure. Ibises and a number of other bird species fed on manure and could become infected. He said it took the birds about three days to die after contracting botulism.
"The birds can't fly anymore and then their legs go lame," he said. "Typically, they get limber neck syndrome as the disease sets in and they can't lift their heads. If this happens to water birds, they can't lift their heads out of the water and they drown."
Rare birds like the Painted Snipe and the Ethiopian Snipe have been spotted at Blouvlei, while the Purple Heron breeds there.