Spoil from dredging would be used for a seawall and a land platform for the wharf which will be restricted to commercial users.
The Vintage Railway component is for a terminus and turntable at the end of the steam engine train line on a site known as the Colenso Triangle, adjacent to the cycle trail and about 100 metres from the proposed oyster operators' wharf.
The beach is eight minutes' walk along the cycleway from the south end of the Opua marina.
Submissions to the resource consent close today.
Frank Leadley, from Bay of Islands Vintage Trust, said the two proposals were not related other than their shared requirement for road access off State Highway 11.
Mr Leadley said the consent applications were combined for cost-effectiveness, on the recommendation of a planning consultant.
Ben Warren, of Ben's Oysters, was unavailable for comment at edition time.
Local residents who want to stop the small bay being converted into a commercial site say they support the Vintage Railway plans.
But the wharf would cover at least half the beach, affect the bay's ecology and cut off the only beach that is accessible to recreational users on the Opua side of Waikare Inlet, they said.
The Save Our Beach group is concerned about the lumping together of the Vintage Railway's plan with the unrelated commercial wharf in the same resource consent.
"We aren't opposed to the proposed railway station and welcome the tourism and visitor opportunities it represents," said Ken Stanton, from the Save Our Beach group.
"We believe the destruction of the beach and its replacement with a marine commercial site has no real relationship with the railway terminus plans.
"Neither relies on the other, and we question the logic in putting these two very different projects into one submission."
Resident Cynthia Matthews said the beach was an asset that complemented tourism and the experience the cycleway provided.
"This area is small but wonderful. It has eco-corridor coastal wetland, mangrove nurseries, rivers, bay and regenerating bush with farm marshland, each supporting varieties of land and water wildlife."
The commercial wharf plan could also sink longer-term tourism proposals, including a jetty at the small headland on the north side of the beach to berth the Minerva steamship, the group said.