The Ruamahanga River and Riversdale Lagoon had a bacteria count that did not meet the guidelines for safe swimming on at least one occasion, rating "D" or "Caution".
The Ruamahanga was also affected by toxic algae blooms over summer.
Also included on the naughty list were parts of Plimmerton Beach, Te Awarua o Porirua Harbour and Titahi Bay in Porirua; Island Bay and Owhiro Bay in Wellington City; Rona Bay, and the Hutt and Wainuiomata rivers in the Hutt.
The online recreational water quality survey http://haveyoursay.gw.govt.nz/rivers-and-coast-users-survey will run until May 13 for people to comment on the results and to get feedback on how, when and where people enjoy the region's rivers and coasts, and what they think about the quality of water.
The council is keen to hear from all ages and there is an opportunity to enter the draw for a 3SIXT HD Sports Action camera or an iPod Shuffle and Bassburger pocket speakers.