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SSA CEO Shaun Adriaanse said the water in the Newton Park Swimming Pool was clear at 22:00 on Tuesday night, but turned green again on Wednesday after another pipe burst overnight.
"I was here twice last night and in the early hours of this morning to check the condition of the pool and everything was on track and it was clear; and then this morning [Wednesday] we had a feeder pipe that supplies water to the area that burst," Adriaanse said.
"There were a few consequences - the water became murkier again and because the water was not circulating we had a build-up of chlorine and it had an effect on the health of our swimmers."
The second day of the championships was postponed on Tuesday after a burst pipe at the pool turned the water green on Sunday.
The water quality caused serious problems on Monday, with competitors struggling to see where they were going and battling with their turns at the wall.
The organisers hoped the six-day championships, which also serve as the trials for this year's FINA World Championships, would resume on Thursday.
There would be only one round in each discipline on the programme, with swimmers competing in timed finals.
"We decided to cancel the program for today, and we are in the process of adjusting it," Adriaanse said.
"We will swim the rest of the program from tomorrow as timed finals, and there is only so far we can go to try and maintain the programme as we (would have) preferred to have swum it.
"Having lost so much time, including today, it would be difficult to manage it in terms of time with heats, semis, and finals."
Adriaanse said the Nelson Mandela Bay municipality had already put measures in place to feed water to the pool through tankers.
"Obviously we are not too happy, our stakeholders are not too happy, but also these things happen and no-one could have planned for a filtration pipe to burst and then a pipe that supplies water to the area to burst," he said.
"It was an unfortunate sequence of events that just happened."
Rising star Myles Brown narrowly missed out on qualifying for the global championships by 0.25 seconds in the men's 400m freestyle on Monday because of the poor water quality.
While the readjusted programme created challenges for swimmers to qualify for the world championships in Barcelona, in July, the selection criteria could be amended and times as far back as the Olympics could be considered.
So far only Olympic gold medallist Cameron van der Burgh has qualified for the world championships in a time of one minute, 00.71 seconds (1:00.71).
South Africa’s other gold medallist at the London Olympics, Chad le Clos, said while the cancellation of the two days was frustrating it would not affect him that much.
"We came here prepared to swim from Monday to Saturday, and Cameron is the only one that has qualified so far, so my spot in the team is not guaranteed," Le Clos said.
"It doesn’t really affect me that much because if I can’t win at nationals, I can’t win at the world championships."
