San Diego Bay tours provide opportunities to sightsee from the water in the form of thrill rides, Champagne cruises, drive-your-own speedboats, and more fun excursions.

Also, many downtown San Diego hotels are within walking distance of the embarkation points for these tours.

See also: Best Downtown San Diego Hotels

You can save on tickets, tours, and hotels through my affiliations. If you make purchases through the links in this post, I may be compensated.

1. San Diego SEAL Tours

The SEAL tour is one of the most popular San Diego Bay tour.

This amphibious bus-boats begins on land and eventually plunges into the water. This harbor tour is a hit with kids, especially.

It runs 90 minutes (30 minutes on land and 60 minutes at sea), is fully-narrated, and currently departs from Seaport Village.

You’ll likely spot sea lions and plenty of birds while learning about San Diego’s history as a military town and snapping plenty of scenic photos along the way.


2. Flagship Cruises & Events

See what the best San Diego Bay Tours are.

Family-owned and operated for over 100 years, this San Diego favorite offers various harbor cruises and ways to tour the San Diego Bay. (Some, I’ve enumerated separately on this list.)

Flagship Cruises options include:

  • Seasonal whale watching tours in partnership with naturalists from Birch Aquarium
  • Sunday prime rib dinner cruise
  • Sunday Champagne brunch cruise
  • Friday Hops on the Harbour (craft beer and dinner cruise)
  • Weekend sunset cocktail cruises
  • Narrated sightseeing tours

Check the Flagship Cruises schedule and then input the date and time you’d like to go.


3. Patriot Jet Boat

The Patriot Jet Boat thrill ride is one of the best San Diego Bay tours.

The Patriot Jet Boat is a 30-minute thrill ride with spins, tricks, and turns around the San Diego Bay at speeds of up to 50 mph. You’ll (quickly) pass by military ships, drive under the Coronado bridge, and be treated to some gorgeous views.

It’s owned by Flagship Cruises and very popular with locals and tourists alike. You’ll laugh, scream and rock out to music during the ride. I always suggest this tour to families visiting San Diego with teens and tweens. Oh, and you will get wet!

There is usually a Groupon for Patriot Jet Boat.


4. Private Water Taxis

If you need to travel between downtown, Point Loma, or Coronado, a private water taxi can pick you up and drop you off.

It’s a fun way to get to your favorite restaurant on or near the bay. You’ll book through Flagship Cruises for a minimum of two hours and it seats up to 33 people.


5. Coronado Ferry

The Coronado Ferry is a way to sightsee on the San Diego Bay.

Take the 15-minute, scenic trip across the bay between Coronado and downtown San Diego. The trip will set you back a mere $5 each way and you can bring on a bicycle for free.

This ferry helps tourists go carless in San Diego. It’s a way to get to the Coronado beaches when staying in downtown San Diego and gives Coronado visitors easy access to restaurants and shops in the downtown area.

Downtown riders catch the Coronado Ferry at the Broadway Pier or the Convention Center. Both departures arrive at the Coronado Ferry Landing.

A seasonal shuttle bus between Memorial Day weekend and Labor Day takes guests from the Coronado Ferry Landing to Orange Avenue (perfect for Hotel del Coronado guests) and Silver Strand (perfect for Loews Coronado Bay Resort guests).


6. Hornblower Cruises

Hornblower Cruises offer some of the best San Diego bay tours.

Book Hornblower Cruises for lovely narrated San Diego harbor cruises for sightseeing, nightly dinner cruises, Champagne brunch cruises, and whale watching tours. Also popular are the Friday and Saturday lobster dinner cruises.

Also keep an eye for their dinner and a movie harbor cruises. The movie shown changes each week. Check their schedule.

Tip: You can book a discounted 90-minute harbor cruise.


7. Speed Boat Adventures

Find the best San Diego bay tours like Speedboat Adventures

Here’s your chance to drive a 13′ mini speedboat as part of a narrated group San Diego bay tour. The boats seat up to three people and are most appropriate for kids ages 5 and older to ride in. Drivers must be 18 years old (age 16 if an adult is present in the boat).

The tour group leader drives usually in the lead and you’ll be able to listen to them talk through a speaker in your boat. Note that you catch this tour this over on Harbor Island, closer to the airport.

Tip: The way to pick your date and tour time at booking is to book direct through Speedboat Adventures.


8. Adventure RIB Rides

Rigid-hull Inflatable Boats (RIBs) have a hard fiberglass hull surrounded by inflated pontoons for extra stability.

RIBs are popular for whale-watching in many parts of the world. These boats, designed originally for military patrols, are smaller and may have a bumpier ride than larger boats.

This smaller, lighter boat may provide more of an up-close experience, but it also may not be for everyone, especially those prone to seasickness.

Adventure RIB Rides usually offers three different tour options: Wildlife and Naval Heritage Cruise of San Diego Bay, Whale and Dolphin Watching (not in the Bay), and a tour of the Los Coronados Islands off the coast of Mexico (but which are visible from coastal San Diego).

Tip: Book their year-round 3-hour whale and dolphin watching tour at a discount.


9. Several VERY Unique Tours on Replica Ships

The Maritime Museum of San Diego maintains replica ships for unique San Diego Bay tours.

America: It’s a 139-foot ship docked at the Maritime Museum available for harbor cruises, whale watching, private charters, and more for up to 80 guests. It’s a replica of the low black schooner famous for winning the historic Royal Yacht Squadron’s 100 Guinea Cup race around the Isle of Wight. That trophy was donated to the New York Yacht Club to be held as a challenge trophy, and it came to be known as America’s Cup. It’s also reported to be one of the smoothest boat rides you’ll ever experience.

Swift Boat: What better way to tour San Diego’s military history than on the Swift Boat, PCF-816. Tours take riders under the Coronado Bay Bridge, the Naval Base San Diego, and the Naval Amphibious Base.

Californian: It’s the Official Tall Ship of the State of California and a replica of a gold rush era revenue cutter. You’ll be able to join the crew in sailing it while learning about San Diego’s maritime history and local marine life.

San Salvador: Sail on a replica of Juan Rodriguez Cabrillo’s ship that carried him to the discovery of California in 1542. This is an ideal opportunity for sailing enthusiasts to experience what it was like on a sixteenth-century galleon over a 4-hour tour.


10. America’s Cup Sailing on the Stars & Stripes USA-11

Be an active participant in a 3-hour, interactive cruise aboard Stars & Stripes USA-11, the same yacht raced by Dennis Conner in the 1992 America’s Cup. You’ll have the opportunity to participate by trimming sails and taking a turn at the helm. Or, simply relaxing is fine, too.

They can accommodate individuals, groups, and charters of up to 24 people. Book in advance, as this is certainly one of the unique San Diego bay tours.


11. San Diego Sailing Tours

Take a 2-hour San Diego sailing tour in the bay.

Grab some friends for a 2-hour San Diego Bay tour via sailboat. San Diego Sailing tours specializes in San Diego Micro-Brew beer and local wines that one may enjoy during the sail from the on-board bar menu.

The captain is happy to narrate historic sites as the sailboat passes by. Private charters are also available.

What are your favorite San Diego Bay tours?