The channel is a significant physical element of NTC. It connects the site to San Diego Bay and provides the potential for multiple uses for residents and visitors. The boat channel covers approximately 54 acres and offers opportunities for recreation, habitat preservation, and development. Additional study and planning are ongoing to determine how the boat channel will be used, whether the sides of the channel (now covered with riprap) should be altered, and what kind of channel maintenance will be necessary. It is currently owned by the Navy.
The channel is essential to the activities of the Ocean Monitoring Laboratory of the City's Public Utilities Department (formerly the Metropolitan Wastewater Department), as well as the Coastal Waters Laboratory that is used by San Diego State University and the U.S. Geological Survey. A pier and boat dock will be constructed to carry out water quality testing and to provide access to San Diego Bay. The integration of the boat channel will also benefit existing and future hotels by offering a waterfront location for pedestrian and recreational use.