At a meeting at the Parua Bay Community Centre in May, the residents said they were told the community would get the opportunity to have their concerns heard when the resource consent application was notified.
However, the residents said only a handful of people were notified in a limited notification.
The residents have concerns about the transfer station being too close to the water and plans to make the site bigger, taking away more valuable space.
Owles said it is in a popular area used by boaties, waka ama paddlers, freedom campers, picnickers and walkers.
"It's a marine and recreation area, with industrial activity. This isn't the place for it."
Owles said they were not trying to shut the transfer station down, but wanted it moved, and said there was an alternative site on Whangārei Heads Rd.
Council chief executive Rob Forlong said the council had consulted on the matter for almost two decades - most recently at two meetings at the Yacht Club and the Parua Bay Community Centre.
"The RMA resource consent process we are currently following stipulates the parties who must be notified."
He said the council was not seeking to expand the range of services at the station, but add another driveway, one in and one out, to improve traffic movement.
Over concerns about proximity to water, Forlong said the council had systems outlined in its resource consent application to prevent pollution.
"This is a transfer station, the rubbish will be moved on every week, it will not be buried there."
The alternative site on Whangārei Heads Rd, near the Nook Rd turn off, was costed at $400,000 but a decision was made not to go ahead with developing that site and instead allocate some of its budget to improving the existing facility at the boat ramp.
Forlong said while some people had told the council it needed to find a better location, it was very difficult if not impossible to find a site that would work.
If the council does not obtain a resource consent, it will have to close the facility and current users will have to take any rubbish and recycling, that does not go out on collection day, into town.