Human sewage was among containments in the water at some Wellington beaches, including Island and Owhiro bays, a report has found.
Rated as the worst spots in the region for swimming, the areas became polluted when heavy rainfall washed contaminants from surrounding urban and rural land into the water, said senior environmental scientist Summer Greenfield.
However, the overall quality of the region's waterways was "generally pretty good over the summer", the Recreational Water Quality report said.
The quality of the water had improved year on year. Only (2 per cent) 30 of the 1697 samples taken during the 2015/16 summer season were deemed unsafe, whereas 58 samples (3 per cent) had been assessed as low quality in the 2014/15 period.
The best swimming spots identified were Princess Bay, Oriental Bay, Mahanga Bay, Worser Bay and Breaker Bay. All of these beaches were all rated with an A or B grade, meaning there was low or very low risk of illness to swimmers.
While most areas were generally safe for swimming, the Greater Wellington Regional Council warned the public to wait two days after heavy rainfall before entering the water, even if the water quality where they were swimming was generally safe.
Testing for this year will begin in December.