Mr Gair said the estuary water was becoming so dirty and shallow that he hadn't seen kahawai chasing sprats there since 2006.
Local sea scouts shunned the millpond-like waters for kayak training, choosing the cleaner water of the beach.
At low tide in summer, the silt fermented and gave off a "dreadful smell".
Milford Residents' Association co-chairman Debbie Dunsford said the estuary upstream from the town centre had been lined with concrete.
"It's an example of what not to do with a creek.
"It serves the biggest catchment on the Shore and filthy silt is washed off and funnelled into the estuary through the piping.
"A terrible smell coincided with the Film in the Park event.
"But I see hawks hovering over it - this is in the middle of the city - which gives hope for improvement.
"As a community, we will be prepared to replant the banks and naturalise the bed of the stream."
The Devonport-Takapuna Local Board voted last month to share half of the study's cost from its discretionary funds in order to get it started.
Council stormwater manager Craig McIlroy said the study would find out whether intervention, such as a new wetland or detention pond downstream from East Coast Rd, would benefit siltation and stormwater quality.
The board has also just approved the Milford Town Centre Plan, after a long community consultation.
The plan calls the estuary and the marina "hidden amenities" near the town centre, where high-rise apartment towers are proposed.
It calls for a healthy and attractive estuary which can take pride of place among the redeveloped centre, beach and reserve.
Plans include an estuary boardwalk and a pedestrian bridge at the northern end.
Milford Estuary
Amenities: Milford Beach, Milford reserve, 220-berth marina, ramp, slipway, sea scout den, pedestrian bridge (proposed).
Problem: 2m-deep mudflats created by silt carried in stormwater drains.
Solution: $20,000 study of the benefit of building an upstream structure to catch silt.
