Fishing bans at Tilligerry Creek and Fullerton Cove, north of Newcastle, will be lifted following investigations into contamination from the nearby Williamtown RAAF base.
The commercial and recreational fishing closures will be lifted almost five years after toxic chemicals used at the base were discovered in groundwater.
There will be ongoing restrictions in place on dusky flathead caught in the Hunter River.
The waterways were closed in September 2015 for testing and analysis of seafood after it was revealed in 2011 that a firefighting chemical used at the nearby RAAF base was found in groundwater and soil.
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