The project's 81-hectare development envelope comprises an entrance channel dredge footprint, offshore disposal area for dredged channel material and seabed levelling in the berth pocket, located in the Shark Bay World Heritage Area and Shark Bay Marine Park.
The proposal involves 80,000 cubic metres of maintenance and capital dredging from the entrance channel of the port and seabed levelling of 10,000 cubic metres in the berth pocket.
The EPA found the proposal could potentially impact marine fauna and fauna from habitat loss, turbidity and smothering.
Marine fauna could also be impacted by noise emissions, vessel strike and entrainment on dredge equipment, and from the introduction of marine species.
There is also a risk of increased tributyltin levels in the berth pocket from seabed levelling of contaminated sediments, which may affect benthic communities and habitats.
Despite the risks the proposal has been cleared, with WA environment minister Amber-Jade Sanderson agreeing the proposal could be implemented, subject to eight conditions including maintaining the environmental values of the World Heritage Area and marine park surrounds.