Organisers said on Tuesday's schedule would be pushed back a day. "We took the decision to postpone the morning and evening sessions to give the municipal staff time to get the water quality up," said Swimming South Africa (SSA) chief executive Shaun Adriaanse.
"Obviously it was not an easy decision to take, but primary in our decision was the swimmers, because with murky water like that there is an element of injury, as they could swim into the wall or the lane ropes.
"Also, it could affect the times that they might possibly swim, so we want to make sure that we do everything possible to give them clear water standards."
Adriaanse said the postponement would affect the programme and the technical team would adjust the schedule. He hoped the six-day meeting, which also forms the trials for this year's Fina World Championships, would be completed on Saturday, as planned.
"One or two events might be swum as timed finals – possibly the longer distance events – and we might have to look at other scheduling in terms of semifinals and final events," he said.
"As it is, we will be swimming tomorrow [Wednesday] morning, whatever the condition of the water, and we had in-depth discussions with the municipality and they've given us their full commitment.
"They are bringing in extra staff and extra equipment to make sure they get the water clean for us."
A burst pipe at the pool turned the water green a day before the start of the championships on Monday.
The South African Polo Championships wrapped up in the same swimming pool on Saturday, when the water was in perfect condition, Adriaanse said.
The water quality caused serious problems on the first day of the championship. Competitors struggled to see where they were going and battled with their turns at the wall.
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.
"To miss out by 0.3 is quite hard and I just couldn't see anything and it is unfortunate that I missed out," Brown said.
Shortly after Monday's evening session was completed, staff started treating the pool to improve the clarity, but by Tuesday morning the murky water had not cleared. Nelson Mandela Bay sport and recreation councillor Marion Harning said the municipality was doing everything possible to ensure the meeting got up and running again.
She said aluminium sulphate was added to the water on Monday night to allow the sediment to settle at the bottom of the pool.
However, the dust particles were too fine for the filters to capture and the municipality had to find other pumps to vacuum the fine sediment.
"Once the swimmers got back into the water the sediment kind of whirled up again, and it's something I haven't seen in all my years with swimming," Harning said.
"We are trying at this stage to contact the swimming pool and filter centre and our own municipal water department, because we need to get the show on the road again tomorrow.
"It is unfortunate that this has happened, but it is just one of those things and we are trying deal with it as best and quickly as we can."
Harning said the city was committed to solving the problem, which she described as an accident. "There is not any blame that I can see that can be attached to any particular person at this stage," she said.
"So we'll just have to get on and do our best to try and remedy the situation." – Sapa