Top End residents have been warned not to swim at Buffalo Creek in Darwin's northern suburbs.
The warning comes after the release of two reports examining the heath of the city's waterways.
The Department of Land Resource Management says the reports show the water quality in Darwin Harbour is generally good, but Buffalo Creek remains in a very poor condition.
Department spokesman Matt Darcey warns the creek is full of bacteria, nitrates and ammonia.
"There is a boat ramp in the mouth of Buffalo Creek and it's used to get access to Shoal Bay," he said.
"We would obviously recommend that people didn't swim in that area.
"Taking fish from the creek itself is probably ill-advised."
The Department says very little can be done to improve the condition of Buffalo Creek.
"At this stage, with the cost of infrastructure and what have you, we're probably stuck with what we have got," Mr Darcey said.
In 2009, another report identified Buffalo Creek as Darwin Harbour's most polluted waterway.
The report said this was mainly because of discharges from the nearby Leanyer-Sanderson sewage treatment plant, which is operated by Power and Water.
At that time, Darwin Harbour Advisory Committee chairman Bill Stuchbury called for immediate action on the problem.
Environmentalists called for improved water treatment and recycling systems to be incorporated in the operations of the sewage plant.