The application will cover all aspects affected by the project including navigational safety, recreational amenities and environmental concerns.
The Planning Inspectorate has 28 days to decide whether the application can proceed to examination.
Before examination can begin, the developers must publicise the application has been accepted by the Planning Inspectorate and include details of how members of the public can register as an interested party.
The Royal Yacht Association (RYA) has announced it will register as an interested party if the plans are accepted.
RYA's cruising manager, Stuart Carruthers, said: "Naturally, if the application is accepted for examinations, the RYA will be registering with the Planning Inspectorate as an interested party in order to represent recreational boating interests.
"The RYA raised a number of navigational issue with the developer during the consultation stage, which were satisfactorily addressed."
Plans for the Navitus Bay development have undergone several changes, most recently in February when the site was cut to 194 turbines from 218 in order for the site to be further away from land.
At the start of April, the developer signed deals with three south-coast ports to explore their potential for becoming the project's operational hub.