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Vessel Entry and Clearance Procedures

Vessel Entry and Clearance Procedures for San Diego Harbor

The following information is provided as a procedural resource for ALL vessels entering San Diego Harbor from foreign waters, and for vessels over 300 gross tons returning from a domestic or international voyage. 

Long term berthing of large vessels   |   619.686.6345 Mon-Fri, 8:00 AM to 5:00 PM.

Pre-Arrival Notice to the National Vessel Movement Center

(Only applies to vessels over 300 gross tons) Vessels over 300 gross tons must notify the U.S. Coast Guard (USCG) National Movement Center (NVMC) ninety-six hours prior to entering San Diego Harbor regardless if the vessel is on a domestic or international voyage.

The NVMC provides assistance 24 hours per day, 7 days a week by phone, email, or FAX.

All time-sensitive inquiries should be addressed to the NVMC via one of the above 24x7 contact methods.

Electronic submittals require an account be generated on the NVMC website at Click on the "Submit to NOA on line" icon to create an account. Then follow the submittal instructions.

Pre-Arrival Notice to U.S. Coast Guard Sector San Diego

(Applies to vessels 100 gross tons or more) (Note: Vessels with fully operational Automatic Identification System (AIS) are exempted from making requests.) Vessels bound for San Diego Bay or Mission Bay shall contact USCG Sector San Diego for permission to enter either by telephone at 619-278-7033 or via Marine VHF-FM Channel 16 prior to entering U. S. Territorial Waters (12 miles offshore). Further radio communication regarding permission to enter the harbor will be moved to Marine VHF Channel 22A.

USCG Sector San Diego Joint Harbor Operations Center (JHOC) Contact Information:

  • Telephone: 619.278.7031 (24 hours)
  • Radio Contact: Marine VHF Channel 16 (24 hours)
  • Address: 2710 North Harbor Drive, San Diego, CA 92101



  • San Diego Bay is served by the San Diego Bay Pilots Association, Inc.
  • The pilot office and boat monitor VHF-FM channel 16 (156.80 MHz) one hour prior to a vessel’s scheduled arrival.
  • VHF-FM channel 12 (156.60 MHz) is used as a working frequency.
  • Arrangements for pilots are made by telephone 619.233.3096 or by calling “Pilot San Diego” by radio; the pilots request the incoming vessel’s estimated time of arrival and draft.
  • A 2-hour advance notice is required if any changes occur.

Pilots board vessels in the vicinity of San Diego Bay Approach Lighted Whistle Buoy 1 (32° 37.3’N, 117° 14.7’W). When boarding, pilots request vessels maintain a speed of 7 knots and rig the pilot ladder about one meter above the water on the starboard side or as directed by the pilot.

The San Diego Unified Port District operates a VHF-FM radio station from Harbor Control Headquarters at Shelter Island for contacting merchant ships, port pilots, and other nearby stations. Channel 16 (156.80 MHz) is for distress, urgent, and safety messages, and for calling; channel 12 (156.60 MHz) is for port operations. The station call sign is KJC-824.

All foreign vessels and vessels from a foreign port or bound thereto, and all vessels over 300 gross tons sailing under register between the port of San Diego and any other U.S. port, are subject to pilotage charges and unless permission is granted from the U.S. Coast Guard Captain of the port shall be under the direction of a federally licensed pilot for the port of San Diego.

Vessels sailing under enrollment and licensed, and engaged in the coasting trade, between the port of San Diego and other U.S. ports, are exempt from all pilotage, unless a pilot is actually employed.

Customs, Agriculture, and Immigrations Services

(This applies to all vessels) All vessels entering San Diego Harbor from an international voyage are required to submit to an inspection by Customs Border Protection (CBP). CBP now provides the combined services of Customs Inspection, Agricultural Inspection, and Immigration Clearance.

Telephone: 619.491-2600  Daily, 6:00 a.m. to 4:00 p.m.
Telephone: 619.550.9079  Daily, 4:00 p.m. to 6:00 a.m.

Commercial Vessel Clearance Location

Commercial vessels should follow their broker's instructions regarding the CBP clearance location upon arrival in the harbor.

Private Vessel Clearance Location

Private vessels returning from foreign waters and requiring CBP services must report to the Shelter Island Harbor Police Dock located at the south end of Shelter Island, 1401 Shelter Island Drive, San Diego, CA 92106. The facility routinely can handle vessels up to 130 feet of length with no pre-notification required. Yachts over 130 feet in length should contact the Harbor Police Communications Center at (619) 686-6272 (24 hour number), eight hours prior to arrival, so that dock space can be cleared to accommodate the vessel. Masters should be aware the water depth adjacent to this dock is 14-feet at MLLW. The dock length is 235-feet. Vessels larger than this should contact the Harbor Police Communications Center for instructions on options to using this dock. Harbor Police Communications will direct vessels to contact CBP to initiate the clearance process. Call the number listed in the Customs, Agriculture, and Immigration Services section above.

ALL VESSELS using the Shelter Island Harbor Police Dock will contact CBP by dialing *82 on the telephone located at the top of the brow to the dock. It will automatically ring through to the CBP inspectors.

San Diego Harbor Police Contact Information:

  • Telephone: 619.686.6272 (24 hours)
  • Radio Contact: Marine VHF Channel 16 (24 hours)
  • Address: 3800 N. Harbor Drive, San Diego, CA 92101 (Headquarters)
  • Address: 1401 Shelter Island Drive, San Diego, CA 92106 (Shelter Island Harbor Police Station)

Quarantine, Customs and Immigration

Pleasure craft and yachts subject to such inspections can make arrangements through the Harbor Police at Shelter Island. Officials usually board documented vessels at their berths. Small commercial vessels and fishing boats are boarded at the B Street Pier. Pleasure craft are boarded at the police berth at Shelter Island. Quarantine is enforced in accordance with regulations of the U.S. Public Health Service.

Agriculture Related Facts

CBP also now provide the required agriculture inspection upon entry into the U.S. from a foreign port. Information regarding agricultural inspections and permitted foods/produce can be obtained by going to the following web site: