Look to Flagship Cruises & Events for the most diverse range of San Diego Bay tours and local insight.

I’ll tell you why BOTH tourists and residents need to keep Flagship on their radar for San Diego bay tours, whale watching, dining cruises, and more. Some offerings may be temporarily modified and you can read more about their safety measures in place. I have a great deal on harbor and other Flagship Cruises tours. If you purchase tickets using links in this post, I may be compensated.

Why Flagship Cruises & Events?

The only place in the world where you can take a Flagship cruise is right here in San Diego. This family business has been a local fixture since 1915.

Flagship Cruises & Events owns and operates the largest and finest fleet in town ranging from luxury yachts to water taxis. Green practices through the use of locally-sourced and sustainable ingredients where possible, shore power to save 2000 hours of generator power, and efficient recycling so guests can feel good about their tour.

Now, the decision to make is how to cruise the bay with Flagship.

See also: Things to Do in Downtown San Diego

San Diego Harbor Cruise

A Flagship Cruises boat sails on the bay during a harbour tour.

This relaxing San Diego Bay tour is a favorite of many local hotel concierges. Those who only have an hour can choose the north or south portion but the two-hour tour covers both. You’ll pass by naval ships and learn about San Diego’s military history (south tour and full tour), admire spectacular views, enjoy our sea life (seals, birds and possibly dolphins), photograph the skyline and so much more on these highly-rated, narrated adventures.

A snack bar serves a variety of sundries including soda, beer, wine, and cocktails so take a seat and enjoy the sunshine while sharing fabulous photos live via complimentary WiFi.

Patriot Jet Boat

Like thrill rides? Then you’ll love the Patriot Jet Boat.

Take a thrill ride on the San Diego Bay with Flagship's Patriot Jet Boat.

Reach speeds of up to 50mph while zooming around the bay seeing in the open-air boat. The narrated tour packs in a decent amount of sightseeing from water (in between a few high-speed 360-degree turns) by taking guests past navy ships, under the Coronado Bridge and more while rock music blares in the background. Ponchos are provided. You’ll get wet but it’s totally worth it.

Coronado Ferry

Take the Coronado Ferry from downtown to Coronado

Did you know that Flagship Cruises operates the Coronado Ferry? It’s partially what makes going carless in San Diego for tourists possible, especially in the summer. The 15-minute ride departs downtown from two locations (Broadway Pier and San Diego Convention Center) and arrives at the Coronado Ferry Landing. Bikes are free to take on board.

From roughly Memorial Day to Labor Day, a complimentary shuttle bus runs from the Coronado Ferry Landing, down Orange Avenue (making the journey easy for guests of Hotel del Coronado) to the Silver Strand where Loews Coronado Bay Resort is located.

On the San Diego side, the Downtown Waterfront Shuttle Bus operates on a loop between the Sheraton San Diego Hotel and Marina that is across the street from the airport and the San Diego Convention Center with a few stops in between. The cost is $3.

Water Taxi

The private water taxi seats up to 33 guests and offers pick-up/drop-off to and from a variety of waterfront hotels, restaurants and sights without waiting in line, traffic or crowds. A 2-hour minimum is required and it’s a great idea for groups and special occasions.

Seasonal Whale Watching

Over 20,000 grey whales migrate from the Bering Sea to the warm waters of Baja California to give birth and make the return journey with their babies in tow.

Flagship offers seasonal whale watching tours between December and April that are guided by Birch Aquarium naturalists. Their “Whale Tail Guarantee” means that if no whales are spotted, guests may join another cruise for free.

Dinner Cruises (Monday – Thursday and Saturday)

Board with a glass of champagne and get ready for a 3-course dinner and fabulous views over a 2.5-hour cruise. A kids’ menu is available in addition to music and dancing. Go on Wednesday for half-price bottles of wine. Saturdays offer a Premium Dinner Cruise option, considered the most romantic dining on the bay.

Hops on the Harbor (Friday)

Join Flagship on Fridays for Hops on the Harbor. Every 2.5-hour cruise features music, dancing, a full bar (that also features a variety of local beers), panoramic views, and a dinner designed to pair with flights from a featured San Diego brewery. The schedule of featured breweries is also online.

Sunday Champagne Brunch

Sunday brunch on a Flagship yacht includes an all-you-can-eat gourmet buffet (all food is prepared onboard) with fresh seafood, made-to-order omelets, carving stations and much more over the course of two hours. You’ll also cruise the bay while sipping bottomless champagne or mimosas. Check out the menu online.

Holiday Cruises

Flagship offers themed cruises in celebration of various holidays like Easter, Mother’s Day and Father’s Day. However, what a killer way to watch 4th of July fireworks than from the Patriot Jet Boat or one of Flagship’s yachts. It’s as close to the show, known as the Big Bay Boom, as you can get.

At the time of this writing, the 4th of July cruise and Thanksgiving cruise are available for ticket purchase.

Luxury Yacht Charters

Flagship Cruises yacht charter at a dock on the San Diego bay.

Perfect for small groups, a luxury yacht like the Quiet Heart takes cruising the bay to a new level with is rich wood finishes, exquisite dining, and access to the captain’s wheelhouse. Or go big with team building or a wedding on the California Spirit, which holds up to 600 guests (300 seated diners). And, they have options in between.

Katie Dillon is the managing editor of La Jolla Mom. She helps readers plan San Diego vacations through her hotel expertise (that stems from living in a Four Seasons hotel) and local connections. Readers have access to exclusive discounts on theme park tickets (like Disneyland and San Diego Zoo) and perks at luxury hotels worldwide through her. She also shares insider tips for visiting major cities worldwide, like Hong Kong, London, Paris, and Shanghai, that her family has either lived in or visits regularly (or both).

Explore More Things to Do in San Diego

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