Wellington City Council says it does not know what effect heavy metals are having on the harbour.
The council is planning to step up its monitoring programme to find out how much oil, petrol, copper and other pollutants are getting in to the water.
Council infrastructure manager Maria Archer says it has spent $70 million over the past 15 years to reduce the overflow of sewage, including faecal matter.
She says 44 cubic metres of sewage flowed into the harbour in the past year, but the level is within required limits.
But while the council's resource consents for discharge allow for a small level of contamination through sewerage, it has now asked for consents which take into consideration other pollutants.
"We know what heavy metals we have but we don't know what the effect on the environment is," Ms Archer says.
She says the city council is waiting for the Wellington Regional Council to decide how often and where it needs to monitor the harbour for those pollutants. She says the council will take action once it knows the scope of the problem.