Sedimentation in many New Zealand estuaries had increased 10-fold over the last 150 years largely due to land clearance and agricultural conversion.
There was increasing appreciation that these fine sediments have major ecological impacts, including preventing light from reaching important ecosystems, such as seagrass, which in turn affected food supply for some fish species and sea birds.
The project, funded by central and regional government, would also see continuous measurement of water temperature, salinity, tidal height, water currents and waves.
The stations would operate continuously, powered by solar panels, and near real-time data will be retrieved remotely.
The data will be used by council staff and Niwa researchers and made publicly available on Auckland Council's website.
It can then be accessed by harbour users to check weather conditions before they venture out.
Andrew Swales, Niwa's coastal scientist co-ordinating the project, said the new stations were important tools in helping resource managers and researchers better understand the processes affecting the Kaipara Harbour.
"These stations comprise state-of-the-art measuring instruments that will give us the most accurate information possible."
Auckland Council senior marine scientist Dr Jarrod Walker said this research programme will provide important data on big weather events which contribute large loads of sediment to the harbour.
Understanding these types of processes are critical in determining where the main sources of sediment are coming from and what can be done to reduce them.
Niwa principal scientist and project leader, Dr Rob Davies-Colley, said that the stations were a crucial part of studies into fine sediment and other pollutants that affect Kaipara Harbour.
The research is also expected to have national significance.
"Diffuse pollutants such as fine sediment, nutrients and microbes are a pervasive problem in many of New Zealand's waters," Dr Davies-Colley said.
"Our estuaries and other coastal waters are often particularly degraded by these land-derived pollutants."
* A public information evening about the monitoring stations will be held this Wednesday, from 7pm at the Mangakura Boat Club, SH16, Hoteo.