13 Best San Diego Harbor Cruises & Boat Tours

Take in the sights and tour the harbor & San Diego Bay in style and comfort with the highest-ranked luxury cruises, joy rides, and informational voyages.
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Experience San Diego by the Sea via Top Harbor Cruises

San Diego SEAL Tour on LandCoronado Bay Bridge at Sunset on Harbor Cruise

The shimmering San Diego Bay is home to placid waves, beautiful sunny weather, incredible views, and lots of wildlife. You can see it all when you embark on a cruise or tour of the harbor, which lets you explore many notable sites from the sea.

The cruises traverse the length of the Embarcadero and the San Diego Bay, starting off in the harbor and heading out into the Pacific Ocean. Take your pick of more standard cruise options with live narration, or look for more unique experiences like jet boat rides, whale watching excursions, dinner cruises, and paddle boat rides. You can even rent out your own sailing vessel and travel at your own pace, or with the assistance of a helpful guide.

Many tours include visits to notable sailing vessels, like those that are part of the Maritime Museum or USS Midway Museum. If a cruise piques your interest and you want to learn more about San Diego’s storied military history, be sure to visit these museums, and grab a Go City San Diego pass when you do!

The Go City San Diego pass lets you book admission to popular attractions and activities for cheaper rates, and you can get an even greater discount when you buy your pass using our discount code.

We’ve selected some of the best cruises offered from San Diego ports so you can plan the ultimate vacation while exploring all the sights these tours have to offer.

Ride in Style on the 13 Best Boat Tours & Bay Cruises

Cruises and other tours through the harbor and San Diego Bay are a great way to get your bearings around the city, especially if you want to learn more about the area.

Many tours have an educational aspect, focusing on the area’s naval history, while others provide soothing luxury experiences, engaging wildlife expeditions, or fast-paced thrill rides.

Sunset Harbor Cruise in San Diego Bay
Sunset Harbor Cruise in San Diego Bay

1) San Diego: Harbor Cruise

Neighborhood: Embarcadero San Diego
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Tour around the beautiful sights of San Diego Bay on the San Diego: Harbor Cruise, which offers all tour-goers splendid views of some of the city’s best coastal sights. These include notable locations like the Midway Aircraft Carrier that now serves as the USS Midway Museum, Coronado Bridge, and a unique view of Downtown San Diego from a distance.

This is an incredible way to explore the city and familiarize yourself with some of its top locations and best beaches so you can better explore them on foot later.

The Harbor Cruise tour lasts for about 1-2 hours, and it’s led by a live tour guide who provides informative voiceover commentary of the various stops on the trip. The tour guide can also point out marine life like sea lions, seals, and the occasional whales and dolphins that are often spotted in the bay.

Sail in comfort on a luxury, modern yacht that includes three levels of indoor and outdoor seating areas. As you take in the view, you can also enjoy the complimentary snack bar, water, and soda, with beer, wine, and cocktails available to purchase.

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San Diego SEAL Tour on Land
San Diego SEAL Tour on Land

2) 90-Minute San Diego SEAL Tour

Neighborhood: Embarcadero San Diego
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SEAL tours are certainly one of the most unique ways to take a harbor cruise, as you won’t just travel by sea, but also by land as well!

The 90-Minute San Diego SEAL Tour hits all the best stops along the Embarcadero and in the San Diego Bay itself too. This is thanks to the unique design of the SEAL tours’ signature vehicles, Hydra-Terras, which are boats with wheels that can carry passengers down the road just as easily as they can ferry you out to sea.

The “SEAL” in the name of the tour refers to “sea and land,” and you’re certain to see all the best sights of each. This is a great tour for learning about San Diego’s significant military history, including its use as a military base through the years, as well as the involvement of ships like the USS Midway in war efforts. In the bay, you’ll see real Navy ships, fishing vessels, and tugboats, offering a truly one-of-a-kind look at the very same historic vessels from the stories told by your live tour guide.

SEAL Tours are family-friendly, and suitable for history and military enthusiasts of all ages.

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San Diego Harbor Cruise on the Spirit of San Diego
San Diego Harbor Cruise on the Spirit of San Diego

3) San Diego: Dinner Cruise

Neighborhood: Embarcadero San Diego
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If you’re seeking a romantic atmosphere perfect for a couples’ retreat, or casual yet elegant ambiance that comes complete with a meal under the stars, you can’t go wrong with the San Diego: Dinner Cruise.

The dinner cruise is actually featured in the Most Fun Things to do in San Diego!

Not only does this harbor cruise let you view notable locations like Cabrillo National Monument and the Coronado Bridge from the comfort of your own private table on a luxury watercraft, you’ll also get to see what the city looks like from afar when it’s all lit up in the evening, with the glow of the lights reflecting on the water. There is truly no atmosphere more soothing in all of San Diego, and this picturesque scene is only complimented by a live DJ setting the stage with ambient music and, of course, some incredible food.

Dine on seasonal dishes and a constantly rotating menu that includes only the freshest produce, meats, and seafood. Dinner is served buffet style with dessert and coffee after the meal, and vegetarian options are available. For an additional fee, you can purchase wine and cocktails from the bar.

Cruises last about 3 hours, and all guests receive complimentary champagne or sparkling cider.

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Sunset on a Harbor Cruise in San Diego Bay
Sunset on a Harbor Cruise in San Diego Bay

4) Sights & Sips 2-Hour Sunset Cruise on San Diego Bay

Neighborhood: San Diego Bay
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While many visitors to San Diego have the chance to watch an ocean sunset on the beach or from the comfort of their hotel room, very few people get to truly experience that sunset by sailing on the bay as the sky starts to darken. You can do exactly that on the Sights & Sips 2-Hour Sunset Cruise on San Diego Bay, which offers an unparalleled happy hour experience!

See landmarks like the USS Midway, Coronado Bridge, and Seaport Village like never before as you take in the view during sunset. Relax with a cocktail on deck as you look out over the waves, then relax and refresh with complimentary appetizers and on-board entertainment.

This 2-hour cruise includes access to a fully-stocked no-host bar with seasonal cocktail specials. Due to the presence of alcohol, the Sights & Sips Sunset Cruise isn’t particularly family-friendly, though it’s a great way to liven up an evening during a business trip, couples’ vacation, or ladies’ weekend.

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Sunset on San Diego Bay
Sunset on San Diego Bay

5) San Diego: Harbor Sightseeing Cruise

Neighborhood: Embarcadero San Diego
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On the San Diego: Harbor Sightseeing Cruise, you won’t just get the chance to see some of the best sights around the bay, you’ll also get to learn about them too! This cruise is led by a knowledgeable live guide who provides an informative tour of many of the bay’s landmarks. There’s no better way to get the inside scoop on famous icons, landmarks, and ships, while also taking in the breathtaking surroundings and soothing atmosphere that’s a natural effect of the ocean.

Points of interest on the tour include Seaport Village, Point Loma, the Cabrillo National Monument, and Coronado Island. Take a 1-hour cruise to the North Harbor or South Harbor, which offer their own unique destinations, or take the 2-hour cruise which lets you see everything!

North Harbor sights include the North Island Naval Air Station, Harbor Island, Shelter Island, and multiple historic ships that are part of the Maritime Museum, while the route through the South Harbor includes the USS Midway, the U.S. Navy Surface Fleet, the Naval Amphibious Base Coronado, and Coronado Bridge.

In addition to historic military sights, look for wildlife native to the bay, such as seals, sea lions, pelicans, and blue herons.

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Whale and Dolphin Watching Cruise Spots a Gray Whale
Whale and Dolphin Watching Cruise Spots a Gray Whale

6) San Diego: Whale and Dolphin Watching Cruise

Neighborhood: Embarcadero San Diego
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Nature lovers are sure to enjoy the San Diego: Whale and Dolphin Watching Cruise, where you’ll have the chance to see these incredible creatures during their peak migration times. This is a great family-friendly activity that kids love, since it offers a unique view into the natural habitats of animals you’d otherwise only get to see at the Sea Life Aquarium or SeaWorld San Diego.

The migration season for gray whales lasts from winter to spring, as the whales move south from the coast of Alaska down to Baja California to calve in warmer lagoons. Meanwhile, tour-goers who book tickets in the summer will have the chance to see blue whales, which can frequently be spotted feeding off the California coast.

Other species often spotted on the cruise include fin, minke, and humpback whales, as well as multiple species of dolphins such as common, pacific, Risso’s, white-sided, and bottlenose varieties.

Tours typically last about 3.5 to 4 hours. They are led by knowledgeable whalers and captains who know where to find not only whales and dolphins, but also sea lions, sunfish, pelicans, gulls, herons, and terns.

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San Diego Champagne Brunch Cruise
San Diego Champagne Brunch Cruise

7) Champagne Brunch Cruise in San Diego

Embark on the ultimate relaxing experience when you book your tickets to the Champagne Brunch Cruise in San Diego!

Not only do you get to enjoy the sensations of the sea breeze in your hair and sun on your face as you cruise around the harbor, you also get to do it in style and comfort while relaxing with a few glasses of champagne and good company.

This 2-hour yacht cruise allows groups to sit at their own private tables with free-flowing champagne or sparkling cider as a non-alcoholic option, all while taking in the sights and listening to a live narration that reveals interesting, behind-the-scenes information about landmarks around the bay. Other alcoholic drinks are available to purchase from the bar during the tour.

In addition to the champagne, guests are also invited to dine on a number of seasonal dishes served in a buffet style. Offerings include a carving station, multiple breakfast and lunch options, pastries, salads, seafood, and a decadent dessert to top off the afternoon. Soothing music completes the ambiance and ensures you’ll experience total relaxation during the cruise.

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Classic Yacht Sailing Experience in San Diego Bay
Classic Yacht Sailing Experience in San Diego Bay

8) San Diego: Classic Yacht Sailing Experience

Neighborhood: Embarcadero San Diego
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Get a taste of the past on the San Diego: Classic Yacht Sailing Experience, where you’ll get to ride in a sailing yacht modeled off ships from the early 1900s.

Tours last 2.5 hours and allow tour-goers to check out nearby landmarks along the coast and in the water, like the USS Midway naval ship. You’ll even have a chance to try your hand at steering the boat yourself!

Tours embark at either midday or sunset depending on your booking preferences, and you can travel privately or share the vessel with other vacationers. The cruise route begins at the Sunset Resort Marina and continues on to the Maritime Museum and Old Point Loma Lighthouse in Cabrillo National Monument.

Note that sailboats have a maximum capacity of up to six people, so the activity is best suited for smaller groups. However, this is a great attraction for families, as adults can relax and soak in the laid-back ocean vibes while kids have fun spotting local wildlife like dolphins, herons, pelicans, and sea lions.

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Patriot Jet Boat Thrill Ride in San Diego Bay
Patriot Jet Boat Thrill Ride in San Diego Bay

9) San Diego: Patriot Jet Boat Thrill Ride

Neighborhood: Embarcadero San Diego
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If you’re craving a more adventurous way to explore the bay, try the high-octane thrills of the San Diego: Patriot Jet Boat Thrill Ride.

During the tour, you’ll ride on an open-air jet boat at breakneck speeds for 30 minutes of fast-paced fun, all while rock music and the salty spray of ocean water against the boat set the scene to perfectly mimic a bombastic action movie. This experience is featured in the Unique Things to Do in San Diego.

While the sheer speed of the jet boat is more than enough reason to give this tour a try, traveling at up to 50 miles per hour and taking 360-degree turns white knuckled is only half the appeal. You’ll also get to see the sights of the bay in a totally unique way. These sights include multiple naval vessels like the Star of India, the USS Midway Aircraft Carrier, and the fleets on display at the Maritime Museum. You’ll also pass by the Coronado Bridge and North Island Naval Air Station.

The San Diego: Patriot Jet Boat Thrill Ride is led by an instructor who ensures guest safety during the experience. All minors must be accompanied by an adult, and ponchos are provided, though you should expect to get wet.

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Drive Your Own Speed Boat in San Diego Bay
Drive Your Own Speed Boat in San Diego Bay

10) San Diego: Drive Your Own Speed Boat 2-Hour Tour

Neighborhood: San Diego Bay
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Are you seeking a more private thrill ride experience in the bay that puts you in the driver’s seat? If so, the San Diego: Drive Your Own Speed Boat 2-Hour Tour is for you!

This tour offers the unique experience of letting you drive around the San Diego Bay in your own speedboat built for two, so it’s very popular with couples and other pairs looking for an adventurous way to explore.

In addition to driving your own speedboat, you’ll also have the benefit of a live guide leading you through the bay in their own speedboat and providing narration through a 2-way communication device. Learn about places of interest like the USS Midway, the San Diego Maritime Museum, and multiple spots along the coast and the Embarcadero. Unlike many other tours, your guide is far from stuffy; they’ll provide witty commentary and interesting stories with a humorous twist while still maintaining the high energy of the thrill ride.

Tours include a safety briefing and instructions on driving the speed boat, as well as a life jacket. Keep a lookout for local wildlife like sea lions and pelicans which frequently make their homes along the shore.

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Mission Bay Private Sun Cruiser Duffy Boat Rental
Mission Bay Private Sun Cruiser Duffy Boat Rental

11) San Diego: Private Sun Cruiser Duffy Boat Rental on Mission Bay

Neighborhood: Mission Bay Park
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While many harbor cruises pack dozens of people onto a larger boat, you can have a more personalized, private experience when you rent your own duffy boat to take out onto the harbor.

With the San Diego: Private Sun Cruiser Duffy Boat Rental, you and your group can relax in the comfort and privacy of this covered passenger boat, with rentals of either 90 minutes or 3 hours. Enjoy the scenery, and keep your eyes peeled for sea lions and seals.

Duffy boats can comfortably fit a maximum of 10 people, making them a perfect family-friendly choice that’s also suitable for small business groups and weekend trips with friends. You’ll have the opportunity to be your own captain, so you can enjoy Mission Bay at your own pace and also bring along snacks and drinks for a picnic lunch on the waves. Best of all, you do not need a boating license to rent a duffy boat, and piloting them is about as easy as driving a golf cart!

All sun cruises come equipped with a Bluetooth system, a covered seating area in case of rain, tables, pillows, and an ice cooler.

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Having Fun with Eco Pedal Boat Rental in San Diego Bay
Having Fun with Eco Pedal Boat Rental in San Diego Bay

12) San Diego Bay: Eco-Pedal Boat Rental

Neighborhood: San Diego Bay
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The San Diego Bay: Eco-Pedal Boat Rental provides a more leisurely way to explore the bay that also appeals to environmentally conscious travelers. Rent a pedal boat and take in the sights, and bring a cooler with water and a picnic lunch for a refreshing meal on the calm waves of the harbor.

This laid-back tour of the bay lets you set your own pace, allowing you to enjoy the sunshine and fresh air from the comfort of the pedal boat. It’s especially popular with families, even those with young children, and each boat can seat up to three adults and one child. In fact, this tour is even pet-friendly, and dogs get their own life jackets just like human passengers!

Boat rentals last for an hour and come with operating instructions and a map of the bay’s landmarks. You can choose where you want to go, traveling between Harbor Island, Liberty Station, and America's Cup Harbor, all while seeking out local wildlife like seabirds and sea lions.

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Sunset Sail in San Diego Bay
Sunset Sail in San Diego Bay

13) San Diego: 3-Hour Sunset Sail

Neighborhood: San Diego Bay
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There are few views as breathtaking as watching the sunset over the harbor, and you can experience this incredible sight in a truly unique way on the San Diego: 3-Hour Sunset Sail tour of the bay.

During the 3-Hour Sunset Sail, you’ll travel around to many of the most notable landmarks both on and offshore. You’ll also get to enjoy an informative narration from your captain, all while watching the sun glint off the buildings of the distant Downtown San Diego area as it makes its steady progress down toward the sea.

Sunset Sail tour groups are limited to a maximum of six people per boat, which makes for an intimate experience. Many couples enjoy the romantic atmosphere, though the tour is also suitable for families. Look out for local wildlife during the cruise, and make use of provided jackets and blankets for added warmth when the bay cools off after sunset.

The cruise also provided complimentary and unlimited soft drinks, water, beer, white wine, and an assortment of snacks.

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San Diego Harbor Cruise by Hornblower Cruises
San Diego Harbor Cruise
All aboard a Hornblower Cruise of the San Diego Harbor with your All-Inclusive Go Pass! Choose from a North Bay or South Bay tour, and check out San Diego landmarks from the ship. Learn from the Captain's commentary and sit back and relax!
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What is a Go City San Diego pass?

The Go City San Diego pass allows visitors to experience more attractions while simultaneously saving money.

With the pass, you can visit San Diego’s top attractions like the San Diego Zoo or LEGOLAND, all while saving up to 55% off on admissions. Plus, the pass gives you the ability to skip the line when visiting select attractions.

Use our exclusive discount code GVSD5OFF to save an extra

Tips for Planning & Preparing Before Your San Diego Bay and Harbor Cruise

Ensure your cruise goes off without a hitch with these helpful tips and important things to know before you book an excursion.

Watch the Weather

Be sure to check the weather leading up to your trip, and keep an eye out for updates from the tour company. While some ships have covers to block out a drizzle and can thus operate rain or shine, others may only run when the weather is nice.

While San Diego enjoys warm weather year-round, there are always a few rainy days, so check each cruise for information about their rescheduling or refunding policies in the case of inclement weather.

Check the Suggested Dress Code

Some, but not all, harbor cruises have a suggested dress code for guests. While these dress codes typically aren’t strict, you’ll want to check them before you arrive so you aren’t too over- or underdressed for your cruise.

Remember that the bay can be fairly cool even on sunny days since there are no buildings to block the wind, so you’ll want to dress in layers with a warm overcoat or jacket.

Watch Out for Limited Wheelchair Accessibility

Some harbor cruises exclusively offer seating on the main deck of the ship, which may only be accessible by staircase or ladder. Other tours have dedicated seats that are accessible for anyone using a mobility device.

Be sure to double check with the tour company prior to booking your ticket if you need accessible accommodations.

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