Both Lake Alexander and nearby East Point beach are officially closed but many people are ignoring advice and taking the plunge.
Darwin City Council tests early last month found bacteria levels on the beach were seven times more than the amount considered dangerous.
The most recent test from the Lake Alexander spillway was nearly double the dangerous amount.
Council water testers say human or animal faeces are responsible for the bacteria but they do not know where it is coming from.
Darwin Lord Mayor Graeme Sawyer wants the Northern Territory Government to test water in the harbour.
"Several times the sea has been way up above the acceptable limits and there have been people swimming in it," he said.
"We need testing regimes in the harbour that run right through the year."
Mr Sawyer says he wants to use DNA testing to work out what is causing dangerous levels of enterococci and E.coli bacteria in the water.
"We have got some really weird readings from the testing that we have been doing around Lake Alexander, including the control site which is in the sea," he said. Read More
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