Multiple Olympic medallist Roland Schoeman wrote on Twitter that a doctor had told him that the dirty water caused his ear infections.
The nationals began on Monday in dark green water at the Newton Park pool after a problem with a filter pipe. They were postponed on Tuesday because of poor visibility and again on Wednesday after another pipe burst.
Officials said they hoped to continue the championships on Thursday, with all events changed to "timed finals." That means competitors will swim only once in each event, with the best time winning the title.
Van der Burgh and Schoeman both posted photos on Twitter of the pool water on Sunday, the day before the nationals, with Van der Burgh comparing the swim meet to an outdoor dam race. Schoeman later said he went to the nearby Greenacres Hospital because of problems with his ears after swimming on Monday.
"Doc says direct result of the water," Schoeman tweeted of his ear problems, for which he has been prescribed antibiotics and pain medication.
Le Clos, who won a gold and a silver at the London Olympics and beat Michael Phelps, is aiming to qualify for the worlds in the 100- and 200-meter butterfly and 100 and 200 freestyle. However, he hasn't been able to swim any of those events at the nationals because of the problems.
The Olympic champion in the 200 butterfly did swim in the heats and semifinals of the 50 fly on Monday, when the water quality caused problems for many swimmers because of reduced visibility.
Van der Burgh, the 100 breaststroke gold medallist in London and world record-holder, swam a world championship-qualifying time of 1 minute, 0.71 seconds in that event despite the cloudy water. Schoeman beat Le Clos in the 50 butterfly semifinals, clocking 23.23 seconds to Le Clos' 23.78.
But the two-delay delay meant Le Clos would get only one chance in the 100 and 200 fly and 100 and 200 freestyle to qualify for the worlds in Barcelona in July and August.
"It doesn't really affect me that much because if I can't win at nationals, I can't win at the world championships," the 21-year-old Le Clos told the South African Press Association.
Swimming South Africa said it was hoping to stage 18 races later Thursday, including the 50 and 100 butterfly, 200 freestyle and 50 and 100 breaststroke.
"Swimming South Africa would like to thank the athletes for their co-operation and understanding," the body said, adding pool management was working "tirelessly" to fix the problems.