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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Gary M
Manteca, California
"Sit back & relax"
TripAdvisor user rating 5 out of 5
Reviewed October 28, 2019 NEW
Took this boat over to Coronado Island. Runs every 25 minutes. $10 round trip. Fast and very nice. Runs from the harbor.
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"A Beautiful Excursion "
TripAdvisor user rating 5 out of 5
Reviewed October 17, 2019
We bought a deal on Groupon to do the 2 hour tour of the north and south harbor. The tour was wonderful! The narrator provided a great overview and we were able to see many attraction! All of the crew were nice and they offer beer and other snacks!
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TripAdvisor user rating 5 out of 5
Reviewed October 10, 2019
Just loved the cruise. A beautiful family business going on for 100 years. The crew is on point! We took the two hours tour & The narrator on board is very knowledgeable. We were lucky to see a dolphin guiding us the way. Boat is super clean so are the seats. A bag check is done before boarding witch is perfect security wise. It’s worth every penny! Thank you crew for this amazing adventure on the bay!
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Casper, Wyoming
"A beautiful way to end the trip"
TripAdvisor user rating 4 out of 5
Reviewed September 24, 2019
The staff truly made this a memorable experience. The ship was very comfortable and we were able to roam about freely; from the upper deck to see the skyline and sunset (as well as a couple of dolphins) and the party deck with a bar and live entertainment, and the deck where we were served dinner. The dinner was great, our server, Tanya, was phenomenal! She was able to handle some difficult customers with a smile and with grace beyond her years and never missed a beat. She was definitely one of the highlights for us!
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Omaha, Nebraska
"Patriot Jet Boat"
TripAdvisor user rating 5 out of 5
Reviewed September 22, 2019
We used the groupon deal to take our friends on the Patriot jet boat. It was very affordable and ended up being one of the highlights of our trip. You will get soaked, even with the poncho. Just come prepared and you will have so much fun. Kind of like a roller coaster on the water.
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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.