Bayswater and Milford marinas were part of a national environmental project on the impact of copper leaching from antifouling paints on vessels' hulls.
NIWA's study found copper concentrations in many marinas could be above guidelines that protect marine aquatic life.
Bayswater got a great report card but Milford had the highest concentration in Auckland, along with Westpark.
NIWA says Milford and Westpark are also affected by urban stormwater and marina hard-stand activities such as boat-washing, scraping and repainting.
The lowest concentrations in Auckland were measured at Bayswater Marina.
It has floating walls but other marinas mainly use solid walls and have small entrances restricting tidal flow.
Port areas predicted to be at greatest risk are Nelson and Milford Sound in Fiordland, a world heritage area.
The modelling work was conducted for New Zealand's Environmental Protection Authority (EPA), which assesses the risk of hazardous substances to the environment.
EPA is also reassessing antifouling paints approved for use in New Zealand.
Antifouling paints are designed to protect the environment by preventing unwanted organisms attaching themselves to boat hulls.
Copper is in almost all antifouling paints on boats and they are designed to leach copper into the water.
Auckland Council's stormwater contaminant scientist, Marcus Cameron, in collaboration with NIWA's Dr Jennifer Gadd and principal scientist Dr Chris Hickey conducted the study.
Mr Cameron says: "The results were quite surprising - the modelling indicated that copper levels could be quite elevated in marina waters and the sampling broadly confirmed that.
"On top of this the estimates of copper being exported from marinas were also significant, with as much copper exported from the four marinas in the Waitemata Harbour as from inputs of stormwater for the whole Waitemata Harbour catchment."
- North Shore Times
Are our classrooms becoming overcrowded?