Harbor guide

San Diego Bay

San Diego, San Diego County, CA

Overview

San Diego Bay is a protected natural harbor about 12 miles long and 1 to 3 miles wide, and it is one of the busiest mixes of recreational, commercial and military traffic on the West Coast. The Port of San Diego and San Diego Harbor Police have jurisdiction over the water, and U.S. Coast Guard Inland Rules apply. The bay is also home to major U.S. Navy facilities, with several aircraft carriers homeported here, so most recreational boating happens alongside warships, cruise ships and cargo vessels.

The entrance past Point Loma

Boats enter around Point Loma, a ridge about 400 feet high. Kelp beds extend more than 1.5 miles south of the point, and Point Loma Light marks the entrance. The dredged entrance channel is 55 feet deep in the approach and 47 feet in the entrance, and it carries 37 to 47 feet through North Bay. Ballast Point, about 1.3 miles north of Point Loma Light, is a narrow choke point where crosscurrents can make vessels sheer suddenly. Zuniga Jetty is submerged and dangerous, and it is marked by orange-and-white signs with flashing lights. The Naval Submarine Base sits just north of Ballast Point.

Where recreational boats go

Shelter Island Yacht Basin and America's Cup Harbor, just inside the entrance, are the most important small-boat areas on the bay, with marinas, yacht clubs, a public launch ramp, fuel docks and the Port's guest docks. Harbor Island, Glorietta Bay in Coronado and the Chula Vista and National City waterfronts offer more marinas and ramps. The Coronado Bridge has 195 feet of clearance in the main channel, and South Bay, south of the Loews resort and Sweetwater Channel, has a posted 5 mph limit and numerous wrecks, shoals and sunken obstructions.

Navy traffic and security zones

Stay at least 100 yards from U.S. Navy vessels and slow to minimum speed within 500 yards. Security zones at Naval Base San Diego, Naval Base Point Loma and Naval Air Station North Island are off limits without permission, and floating barriers mark some of them. A restricted area south of Ballast Point allows temporary mooring of up to 24 hours but not permanent anchoring. Vessels under 66 feet and sailing vessels must not impede large commercial or naval ships in the channel.

Anchoring and guest docks

Anchoring is limited to the Port's designated anchorages, which require a free permit, and a holding tank is mandatory. The Port also rents 26 guest slips at Shelter Island for up to 15 days in a 40-day period.

Getting there & access

Entering from sea

Approach from the south or west around Point Loma and give the kelp beds and Zuniga Jetty a wide berth. Follow the entrance channel past Ballast Point, where crosscurrents are strong, and keep clear of large ships and warships that are confined to the channel. Small vessels under 66 feet and sailing vessels must not impede large vessels that are confined to the channel.

Navy zones and VHF

Do not enter security zones around Naval Base San Diego, Naval Base Point Loma or Naval Air Station North Island without authorization. To ask for passage, call the Coast Guard Captain of the Port at 619-683-6495 or VHF 16 (Naval Base San Diego zone), Coast Guard Sector San Diego at 619-278-7033, or Navy Port Operations at 619-556-1433 on VHF 16 or 12. VHF 16 is distress and calling, 13 is bridge-to-bridge, and 12 is Navy Control. The Port also operates a station at Shelter Island using 16, 12 and 17.

Guest docks and customs

The Port's guest docks are at 1401 Shelter Island Drive at the entrance to Shelter Island Yacht Basin. Reserve online at reservations.portofsandiego.org or call 619-686-6227. Recreational boats arriving from foreign waters must clear with Customs and Border Protection at the Shelter Island Harbor Police dock at the same address; Harbor Police dispatch is 619-686-6272.

Anchorages

A-1 La Playa Cove (Shelter Island Yacht Basin) is a 72-hour, weekend-only anchorage from Friday 0900 to Monday 0900, with 96 hours on holiday weekends. A-5 Glorietta Bay in Coronado allows 24 to 72 hours, seven days a week. A-9, the Cruiser Anchorage at the eastern tip of Harbor Island by the Coast Guard Air Station, is for non-San Diego County residents only: up to 90 days in a 365-day period, with permits renewed every 30 days after an in-person Harbor Police inspection. Reserve A-1 and A-5 online at least 24 hours ahead. The Port closed the A-8 anchorage in 2008.

By land

Shelter Island Drive runs the length of Shelter Island and is the road access to the marinas, ramp, fuel docks and guest docks.

Amenities

  • Guest docks — 26 slips for boats up to 65 ft at 1401 Shelter Island Dr, with water and 30-amp power; $1.51 per foot per day as of 7/1/2026
  • Public pump-outs — Shelter Island Harbor Police and guest docks (four stations, 24 hours, no fee), Sun Harbor Marina, and Harbor Island West Marina fuel dock (24 hours, no fee)
  • Fuel docks — Pearson Marine Services (2435 Shelter Island Dr), High Seas Fuel Dock (2540 Shelter Island Dr) and Harbor Island West Marina (2040 Harbor Island Dr)
  • Public launch ramps — Shelter Island (free), plus Chula Vista, Glorietta Bay (Coronado) and National City
  • Marinas and yacht clubs — Shelter Island Yacht Basin, America's Cup Harbor, Harbor Island, Glorietta Bay and the Chula Vista and National City waterfronts
  • Dock and Dine — More than 60 waterfront restaurants accessible by boat, listed by the Port
  • Bait barge — Everingham Brothers Bait Barge on the right side of the Shelter Island channel, 24 hours

Rules & official resources

Common boat service needs here

Hull cleaning and bottom paint

Boats kept in slips around the bay need regular hull cleaning. Copper antifouling paint is under pressure at Shelter Island Yacht Basin because of a copper pollution limit, so many owners ask for low-copper or non-copper bottom paint when they haul out.

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Engine service for channel conditions

Crossing the busy channel, Ballast Point crosscurrents and the run to the open ocean put steady hours on engines. Owners need reliable cooling-system, impeller and fuel-system service.

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Electronics and radios

Navy zones and mixed shipping traffic make a working VHF and good navigation electronics worthwhile.

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Sun and salt care

Constant sun and salt spray wear out canvas, cushions and gelcoat. Detailing and canvas replacement are routine for slip-kept boats.

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Surveys and sales

Buying or insuring a used boat on the bay usually calls for a pre-purchase or insurance survey.

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Guides & FAQs

Nearby providers

No providers listed near this location yet — check back soon.

Sources