Winter Whale Watching Adventure by Flagship in San Diego, CA

Flagship Cruises & Events990 North Harbor DriveSan Diego, CA 92110
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Presented by Flagship Cruises & Events, Whale Watching with Birch Aquarium offers two types of whale watching experiences for guests of all ages. From December through April, these experiences can be had on the twice-daily cruises that depart from the San Diego Harbor, featuring stunning views of and detailed information about gray whales throughout the three-and-a-half-hour tour.

Good To Know

from Ashley, one of our San Diego Travel Experts
  • Seating is first come first serve basis.
  • Dress in layers - temperature and wind are unpredictable.
  • Bring camera and binoculars.
  • Guarantee of seeing a whale.
  • Tours only from mid-December through April.


from Winter Whale Watching Adventure by Flagship
Each year approximately 20,000 gray whales migrate from the Bering Sea to the lagoons of Baja California and back again. From December through April you can witness this amazing journey off the coast of San Diego on educational whale watching excursions with Flagship Cruises & Events and our partner of over 14 years, Birch Aquarium. According to our partner, optimum whale migration viewing times are late December through January during the southward migration.

Flagship Cruises & Events along with Birch Aquarium is proud to provide two types of whale watching experiences, both leaving daily from the San Diego Harbor. Whichever one you choose, you will have an experience of a lifetime!

Join Birch Aquarium naturalists and Flagship Cruises & Events as we venture out for twice-daily cruises to locate gray whales on their annual round trip migration from December through April. Get a close-up look and learn about gray whale baleen, barnacles, and prey items from the naturalists during the 3.5 hour tour.

Crunched for Time?
A new addition to our fleet is our High Speed Jet Boat, the Patriot. The Patriot will take you out to see the majestic whales and other marine life such as seals, sea lions, migrating birds, and more in half the time!

Tripster Customer Reviews

2 Reviews
Tiffany Christy
Mandeville, LA
1 Review
Verified Traveler
"Worth it"
January 2018
They were very informative and the ride was long. Well worth it
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Renee Maxfield
Oceanside, CA
1 Review
Verified Traveler
"A Fun Day"
February 2015
We saw gray whales and dolphins. Boarding and departure were timely, staff very courteous and informative. And the ocean was so calm that day. Everything just went really smooth.
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TripAdvisor Reviews
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Gloucester, Virginia
"Very Infomative"
TripAdvisor user rating 5 out of 5
Reviewed September 14, 2019 NEW
Nice view from the top deck, we booked the two hour tour we went North then came back within the hour not exactly sure what was going on the narrative announced they would be dropping of and picking up passengers for the tour going south (the next hour) I guess they do that all day because as we got off it was going north again. So if you get on and are heading back after and hour dont worry, the narrator which I cannot remember his name was excellent very knowledgeable of the area, the ships and the area. Truly wish I could remember his name reminded me of a old salt sailor. We did see some Sea Lions on the North trip which I would guess is the norm they were located near the live bait area. If you only have a short visit and you want to see a lot of the Harbor I would definitely recommend the tour.
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Willard, Utah
"A breath of fresh air"
TripAdvisor user rating 5 out of 5
Reviewed September 12, 2019 NEW
I was going back and forth debating what brunch cruise me and my husband should take. I am so pleased that I choose Flagship Cruises. We had a beautiful table next to the window and seated with three amazing couples. It was so delightful to get to know them and their backgrounds. Honestly, the cruise might have been a little boring if we had not been seated with others. There were endless Mimosa and champagne. Caviar was good, the brunch was great and lots of variety. I didn't get pictures of the food because I was filming live on FB. But what a beautiful ship! The only thing I have to complain about was we paid for our picture but never received it, but that was the only thing. It was a little hectic and we were the last ones off the ship, so our server might have just overlooked it. Anyways, I would recommend the brunch cruise, yes it's a little bit of money but for food and a cruise, it's worth every penny! Oh, and the service was amazing.
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Caroline L
Los Angeles, California
"Patriot Jet Boat is a Blast! "
TripAdvisor user rating 5 out of 5
Reviewed August 18, 2019
Tips before ride: purchase on Groupon for a discount, bring a small towel, and get in pre-boarding line early (30 minutes before). We got an excellent deal through Groupon and decided this looked like a lot of fun. It also seemed pretty unique since this is the first time we had seen a boat of this caliber hold so many people. Unfortunately we were almost at the end of the line to board which meant we got the seats which I presume get the most water. If you don’t want to get soaked, the closer you are to the front the better chance of not being drenched. They do hand out recyclable ponchos but it’s likely the water is going to find a way in. Upon the first turn, we had what looked like a small tidal wave come into the boat. We were soaked and our eyes were burning from the salt water. It was pretty funny. The music that plays is hardly audible because the engine is so loud but you will quickly forget about the music as you struggle to keep your poncho in place. It’s a truly one of a kind experience and we were so glad we did it. The staff was very kind and helpful.
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Susan S
Philadelphia, Pennsylvania
"Ferry from San Diego Harbor to Coronado was great."
TripAdvisor user rating 5 out of 5
Reviewed August 18, 2019
At only $5 each way, The boat was lovely and clean. We went right by the Midway Aircraft Carrier Museum and it is even more imposing from the water. The ride to Coronado was short, scenic and lots of fun. Highly recommended.
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Chino Hills, California
"Patriot Jet Boat is Awesome!"
TripAdvisor user rating 5 out of 5
Reviewed August 08, 2019
Great crew, fun music and the beauty of the Coronado Bay in a speedboat - what else could you ask for? We had a great time. You will get wet so plan accordingly. Open through Labor Day.
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Winter Whale Watching Adventure by Flagship is located at Flagship Cruises & Events990 North Harbor DriveSan Diego, CA 92110
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Frequently Asked Questions about Winter Whale Watching Adventure by Flagship

Do you really see whales?
Yes. San Diego is one of the top gray whale watching destinations in the world.

Do you see more whales in the morning or afternoon?
Your chances of seeing whales are the same on the morning or afternoon cruise.
What day of the week is better?
Your chances of seeing whales are the same no matter what the day of the week, however, weekend tours tend to be more crowded.

Where should I park?
Gated paid parking is available at the Five Star parking lot next door on the Naval Pier (next to the USS Midway), at the Cruise Ship Terminal Pier (B street) and off Pacific Highway at the corner of Broadway and Pacific Highway. Look for “Cruise Ship Terminal” Parking.
  • 5 Star Parking (Corner of Broadway & Pacific Highway) - $12.00
  • USS Midway Parking lot - $7.00 for first 4 hours, $10.00 for 10 Hours, $12.00 all day
  • B Street Pier Parking lot - $12.00 all day 
  •  Limited metered parking is also available for $1.50 per hour (2 hour max.)
*Parking rates subject to change*
What else do you see?
In addition to California gray whale adults and calves, you could also see finback whales, blue whales, humpback whales, minke, killer, and false killer whales. Additionally, you could see pods of hundreds of dolphins including risso's, common, and white sided, and other marine life such as sea lions and a variety of coastal birds.
Is smoking allowed?
No, smoking is not allowed on the vessel.
Why are you different from other whale watching companies?
Flagship Cruises & Events is the only company whose tours are guided by experts from Birch Aquarium at Scripps, now celebrating our 14th year of partnership. Proceeds from each tour help support Birch Aquarium at Scripps’ education and conservation programs.
How far will we cruise into the ocean?
In the beginning of the season, the southbound whales swim closer to the coast, so the maximum distance is about 3-5 miles. Toward the end of the season, when the northbound whales swim further out, we can cruise up to 9-12 miles off the coast.

Can I touch the whales?
Should I make reservations?
Yes. Reservations are strongly recommended due to the popularity of this tour. There is the chance we will sell out on busy days, especially on the weekends.
What should I wear?
We suggest dressing in layers, as the temperature/winds are often unpredictable. Be prepared for cool weather even if it’s sunny out side. It is also recommend you bring sunscreen and a hat.
What time should I be there?
Allow enough time for traffic, find parking and to check in for your boarding pass. The morning cruise boards at 9:15am and the afternoon cruise boards at 1:00pm. Seating is on a first come, first served basis. If you prefer a specific seating area, be early so you can be the first in line.
Where do we board?
Boarding is located at 990 N. Harbor Drive, at the corner of Broadway and Harbor Drive. Look for the ticket booth with the black awning for check in.
Can I bring food or drink on board?
No. However, for your convenience, we have a snack bar plus hot and cold beverages available on board for purchase.

Are your whale sightings guaranteed?
Yes! That means if you don’t see whales you will be issued a "whale check" that is good for another whale watching cruise, good for any day of the week. Or, if you prefer, you may request a ticket for a 1 or 2 hour narrated tour instead.
Will I get seasick?
If you tend to have a problem with motion sickness, there is a chance you could get sea sick. It is recommended you take any medication before boarding the vessel. Wrist bands for motion sickness also work well. Either can be purchased at most drug stores.
What if it rains?
Tours are not necessarily cancelled due to rain, however if there is a wind advisory or if weather conditions are extremely poor, then it’s possible the tour will be cancelled by the Captain the morning of. We will do our best to contact you with the phone number you provide if a tour is cancelled. Should your tour be cancelled then you have a choice to either reschedule your tour for another date, or receive a full refund.
Are your boats safe?
Yes, all of our vessels are inspected regularly and are 100% Coast Guard Certified.
Is seating indoors or outdoors?
We provide both indoor and outdoor seating on our vessel.

Is the boat wheelchair accessible?
The vessel and interior main deck are ramp accessible, however the exterior top deck and restrooms are not.