Explore San Diego Harbor with Flagship Cruises San Diego
There’s something so special about seeing our beautiful San Diego from the water! When family and friends come to visit, we always suggest a harbor cruise and despite having been on many of them, I am still excited to go on another one. Recently I was invited on a cruise around San Diego Bay, the Flagship Cruise San Diego, our favorite San Diego harbor cruise.
It’s an ideal way to get the lay of the land, but also to take in the magnificent views that make San Diego such a fascinating city. And as locals, we love it too – for the history, tales, and sights we discover. And of course, the experience of being out on our picturesque San Diego Bay.
It’s a must-do for anyone who loves being outdoors and on the water. With San Diego’s practically- perfect weather year-round, any season is ideal for a harbor adventure.
FAQs about the San Diego Flagship Cruise
Since 1915, Flagship Cruises has been offering a multitude of harbor excursions and adventures for locals and visitors. They are San Diego’s longest-running harbor tour company.
One of our favorites is the combination Two-Hour, Full-Bay harbor tour on the Spirit of San Diego, Flagship’s second-largest yacht. This cruise offers guests the best of both San Diego’s north and south scenic spots, all expertly narrated by a knowledgeable guide in a relaxed, comfortable setting. We have been on both day trips and sunset sails, and though they’re both phenomenal, our last sunset trip was spectacular. It didn’t hurt that Mother Nature was very cooperative – full explanation to follow!
You can book tickets in various ways. You can buy tickets in person at the booth right by the San Diego Harbor. However, I recommend booking them in advance. Especially right now with limited capacity to ensure social distancing and in the summers during the high season, tickets can go days in advance. I often find great deals on Groupon and Viator. Take a look here to find great deals:
– Dinner Cruise
– Brunch Cruise
– Hops on the Harbor
– Whale Watching
– Jet Boat Thrill Ride
– Whale-Watching and Jet Boat Combo Ticket (Cheaper!)
There are six daily tours, and though walk-ons may be accommodated, advance tickets are highly recommended (especially with decreased COVID-19 capacity). Guests may also choose a one-hour northern or southern route if time is limited.
Masks must be worn when boarding and while on the ship, except when eating or drinking. As already mentioned, there is a reduced capacity on the cruise to ensure social distancing. 
The cruise departs from the San Diego harbor and guests should arrive 15 minutes before boarding.
Metered parking is available along the waterfront with a three-hour maximum. The closest flat-fee parking lot is located next to the USS Midway where $10 will provide up to 12-hours of parking. This is our best recommendation, especially for those planning to have lunch or dinner before or after their cruise. And why not? You’re on the waterfront after all.
While onboard, guests have the option of three decks of spacious indoor and outdoor seating. The open-air upper deck is best for 360-degree viewing and photo ops. There’s also an onboard snack bar in addition to a full-service bar.
We recommended packing a hat, sunscreen, sunglasses, and a windbreaker or light jacket as the bay can get a bit breezy at times. And don’t forget your camera. Views are incredible!
North Harbor Sights
Heading along the northern route, our cruise offered stunning vistas of the San Diego skyline as we sailed past the historic Star of India, the world’s oldest active sailing ship and other iconic vessels of the San Diego Maritime Museum. Among their historic nautical treasures are the HMS Surprise (featured in Pirates of the Caribbean and Master & Commander), and the intriguing B-39 Soviet submarine.
Our next vista point was Harbor Island, a man-made peninsula created in 1961 from harbor dredgings. It was awesome passing some of our favorite waterfront restaurants along the way like Island Prime/C Level and Coasterra. Sea lions were the stars of the show near the Point Loma Submarine base, attracting the attention of both big and little kids alike.
Shelter Island is amazingly picturesque from the water with its marinas and throwback touches of aloha in its restaurants and hotels. It’s fascinating to see the U.S. Navy carriers along the coast of North Island Naval Air Station, along with other naval vessels transiting the waters of the bay.
We returned momentarily to our debarkation peer to drop off northern route passengers and pick up one-hour group for the southern portion of our excursion.
South Harbor Sights
Flagship’s southern route introduces passengers to the U.S. Navy fleet. Queen of the route is the majestic retired U.S.S. Midway aircraft carrier. San Diego is and always has been a beloved Navy town, and it’s evident why as we cruised past a host of warships of all shapes and sizes piered along the naval base. On a clear day, Mexico can be seen in the distance, a mere 14 miles away.
The southern route also features views of Coronado Island with its waterfront restaurants and hotels. Coronado is technically not an island as it’s connected to the mainland by a narrow strip of beach. But as our guide exclaimed “Don’t tell the locals. They believe this magical place really is an island!”
Amphibious Base Coronado is the renowned home of the Navy SEALS, who train along beaches of the island. The crowning moment of the cruise (and one we’re always excited about) is passing under the massive Coronado Bay Bridge.
This architectural masterpiece, one of San Diego’s most iconic sites connects downtown San Diego with Coronado Island. Extending 2.1 miles over the San Diego Bay, it’s 200-foot-high vertical clearance allows any ship to pass easily underneath its span. Views of this magnificent sweeping curved bridge are spectacular from the water.
As we slowly cruised back to port, we couldn’t have been more pleased with this perfect ending to the cruise. For as the sun set over the horizon, the San Diego sky was lit ablaze with a painter’s palette of amazing vibrant colors.
A perfect ending to a perfect cruise.
Other Flagship Tours and Cruises
Flagship’s fleet of vessels offers many other cruises for those who love being on the water. Here are some more really great Flagship Cruise San Diego options:
Coronado Ferry – a round-trip scenic boat ride across the bay servicing both San Diego and Coronado.
Dining and Drink Tours– Include a myriad of dinner cruises, Sunday champagne brunch, a Friday “Hops on the Harbor” featuring local brews and foodie offerings. Their “Spirits at Sunset Cocktail Cruise” will return in summer 2021.
Whale Watching – December through April offers the chance to view gray whales migrating along the Pacific Coast (along with dolphins, sea lions, and more). Flagship cruises offer a whale-watching cruise with naturalists from the Birch Aquarium that will tell you lots of interesting information about these amazing animals. Book your tickets here>>
Patriot Jet Boat Thrill Ride – for the more adventurous! This turbo-charged 30-minute tour offers speed, screams, splashes, and sharp dramatic turns in a powerful open-air jet boat. Book this thrilling adventure here>> And if you plan to go whale-watching AND on the Jet Boat ride, you can save some money by buying the tickets together. Click here to save some money!!!
With so many San Diego Flagship cruise options for being on the water, the choice is up to you. Enjoy!
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