Portbury Wharf Nature Reserve was created by North Somerset Council as a buffer between new homes and the port.
A residents' levy to fund the site, managed by Port Marine Management Ltd (PMML), was scrapped in 2015 after complaints about cost.
The council will now need to agree the deal with the founding PMML directors.
Permission for 2,600 nearby houses was granted to developer Persimmon Homes as long as the reserve was created.
PMML was formed to collect the levy and operate the site - but the levy rose from an initial £12 to £70, prompting calls for more transparency.
Until the end of 2015, PMML commissioned Avon Wildlife Trust to manage the land for £75,000 a year with staffing.
After this agreement ended, the council stepped in while it could find a long-term solution.
The council's policy committee report concluded PMML's structure was a "mess" and "not fit for purpose" and the best option for the reserve was to allow the council to manage it.
If PMML's current directors - North Somerset Council leader Nigel Ashton, Chris Giles and Arthur Terry - agree, £400,000 collected from the levy will now need to be transferred to the council.
This fund will pay for the upkeep of the reserve for the next 10 years.
This story was updated on 5 May, 2016. The original version wrongly reported PMML's original directors, David John Smellie and Richard Graham Winborn, would have to agree to the £400,000 to be transferred to the council.
The best option to safeguard a coastal nature reserve is to allow North Somerset Council to run it, a report has concluded.