Sea of Cortez Cruises – A Complete Guide to Ports, Routes, and Adventures

The coastline of Baja via UnCruise

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A Sea of Cortez cruise is an intriguing way to visit “the world’s aquarium,” in the words of Jacques Cousteau. It’s a nature lovers’ paradise, with one-third of the Earth’s marine mammals, 900 species of birds, crystal blue water, and deserted white sand beaches.

This article covers the port-of-calls and overnight anchorages you’ll find on a Baja Mexico cruise for both mega cruise ships and smaller boutique adventure cruises, including interactive maps and a focus on shore excursions. Keep reading if you ever dreamed of following in the footsteps of Steinbeck or Cousteau through one of the most biologically diverse regions of the planet.

Guest kayaking with Safari Endeavour in Agua Verde via UnCruise
Grey Whales in Magdalena Bay

Sea of Cortez Map

Below is our Sea of Cortez map that accompanies this post. It has a typical mega cruise route and boutique cruise route, including port of calls and shore excursion options. It will not help you navigate the Gulf of Mexico, but it might just help you decide if you want to go cruising. If it doesn’t load, you can hit the refresh button or click this link. Either way, we encourage you to click around a bit and take a digital Sea of Cortez cruise.

It’s laid out similarly to this post, where you start in Cabo San Lucas and travel across to the Mexican Riviera for calls in Mazatlan and Puerto Vallarta. You return to the Baja in La Paz and make your way up the islands of the Gulf of Mexico until you reach Loreto.

Cabo San Lucas

Many Baja Mexico cruises start at Cabo San Lucas, with its massive cruise port and the Los Cabos International Airport. The flights are reasonable, too, with direct round trip tickets from several US cities costing less than $200 and taking less than 3 hours in the air

If you’re on a mega cruise, you’ll likely be responsible for the 30-mile (~$60) transfer from the airport to the cruise port and perhaps a night at a resort on the front of your trip. Boutique cruise brands like UnCruise do things differently, including partnering with a resort close to the airport and packaging in airport shuttles.

Cabo and the Mexican Riviera ports of Mazatlán and Puerto Vallarta have formed a cruising triangle for decades and developed a healthy shore excursion industry. Many boat tours depart from the harbor, ranging from kid-friendly pirate boats to romantic sails. Every boat of every flavor takes you by the famous Cabo Arch, which sits just outside the harbor. From there, they go to Lover’s Beach, adjacent to the Arch, or more distant beaches like Playa Santa Maria or Chileno Bay, where they offer swimming and snorkeling. Sometimes, they cruise the coast looking for whales or dolphins.

Overland adventures feature short trips to one of Cabo’s many resort hotels or bus tours 75 miles north to Todos Santos to find an “authentic Mexican experience.” Adventure parks, like Wild Canyon Adventures and Canopy Costa Azul, offer zip lines, rappelling, ATV tours, and more.

Cabo Arch via Canva
Shopping in Cabo via Canva

San José del Cabo

Like our Baja UnCruise, boutique cruises utilize Cabo’s well-developed infrastructure differently than mega cruises. They have partnered with the Barceló Grand Faro Los Cabos, an all-inclusive beach resort, for staging before and after the voyage and worked it into the trip’s price, including transportation.

A shuttle bus was waiting for me at the airport, which took me directly to the resort. We spent the night on the arrival day, where I had full use of the facilities, including buffets, pools, and a private beach. We also returned to the resort mid-morning on the departure day. Several people on my cruise planned their flights around the resort days so they could have time for off-property adventures. The Concierge desk at the Barcelo will happily arrange activities, like the adventure parks, or you can walk 1/2 hour into downtown San José del Cabo (or grab an Uber) for some shopping and Mexican culture.

Barcelo Gran Faro Los Cabos Resort - resort pool

Mazatlán

Do you remember that “Cruise Triangle ” between Cabo, Mazatlán, and Puerto Vallarta? Here’s the rub. Two of those three ports (Mazatlán and Puerto Vallarta) aren’t in the Gulf of Mexico or the Baja at all. They are on the mainland in the Mexican Riviera. The ocean floor outside Cabo drops quickly to 1200 feet, which isn’t good news for explorers of “the World’s Aquarium” since 90% of the fish live above the continental shelf. However, they are included on most mega cruise itineraries, so we’ll cover them here. Plus, you’ll have a chance to see tropical jungles and different indigenous influences, such as Papantla Flyers.

See also
8 Differences Between Mega Cruising and UnCruising That Show Bigger Isn't Always Better

Mazatlán is almost 500 years old and home to half a million people. There’s a plethora of tours ranging from hiking to the lighthouse (Faro Mazatlán) on a hill overlooking the cruise port to venturing into town to see the Plaza Machado, Malecon de Mazatlán, Cathedral Basilica de la Inmaculada Concepción, and other sites of this ancient city. There’s also a beach excursion to Stone Island, but that was the lowest-rated excursion offered, and you’ll find better beaches at other stops.

Inland excursions include a bus trip to the villages of Concordia and Copala to see life in the foothills of the Sierra Madres, including adobe brick-making demonstrations, pottery, and historic churches. Of course, there’s a zip line option too, but the most popular and highest-rated excursion is the salsa classes at a nearby resort. Which salsa? How about both? You’ll learn to make the traditional Mexican dish and dance the Latin dance. It’s perfect for people who can’t make up their minds, but its popularity and rating also speak magnitudes about the things to do in Mazatlán.

Mazatlán sign via Canva
Salsa Dancing via Canva

Puerto Vallarta

Puerto Vallarta, or PV for short, was a sleepy village until American tourists discovered how beautiful it was. Even though its bay, Bahia Banderas, is one of the largest bays on the Pacific Coast, the port up the coast in San Blas handled the majority of the traffic because of overland routes to Guadalajara.

John Huston’s 1964 movie, The Night of the Iguana, introduced PV to America, and the cruise lines were enthralled with the natural beauty, deep water port, and undeveloped land. Today, more than 450 thousand cruise passengers visit PV yearly, and they’re welcomed by a healthy shore excursion menu.

The most popular shore excursions in Puerto Vallarta are city tours where you see some combination of Elizabeth Taylor’s Gringo Gulch, the historic waterfront, churches, and tequila tasting.

There’s plenty of adventure to be had in PV. It’s home to Los Veranos Canopy Tour, allegedly the largest zip line tour in the world. Their 19 lines through the tropical jungle sound like heart-pounding fun with an exotic view, but Banning Mills in Georgia holds the world record for World’s Longest Zip Line Canopy Tour, with over 100 lines traveling more than 11 miles through the air. Still, 19 lines through the jungle canopy is impressive, plus e-bike tours, hiking tours, and river play make a day at Los Veranos good clean fun.

You can also take beach excursions from port ranging from exclusive beach resort getaways to boat tours of remote bays like Playa Majahuitas and Playa Yelapa to snorkeling in the tropical waters off Islas Marietas.

Puerto Vallarta sign via Canva
Puerto Vallarta via Canva
Los Veranos Canopy Tour Puerto Vallarta via Canva

La Paz

La Paz is a much less frequented destination for mega cruises than the “Cruise Triangle.” It saw 21 cruise ships arrive during 2022, which is fewer than dock in Cabo San Lucas every month! However, that will soon change as the newly expanded Pichilingue Cruise Port gains popularity.

For now, there are limited excursions, including scenic drives, artisans & shopping, and highlights of La Paz, including the Cathedral Nuestra Señora de La Paz and Baja California Sur Regional Museum. It isn’t hard to imagine these experiences getting more synthesized and nature-based excursions growing, including whale shark watching, snorkeling with baby sea lions at the nursery off Los Islotes, and exploring the natural paradise of Isla Espiritu Santo
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The environmental impact of the La Paz cruise port could forever change a pristine natural sanctuary, or it could be a window to the world where people learn and practice ecotourism. Currently, 244 islands and associated marine areas form the Islands and Protected Areas of the Gulf of California UNESCO Biosphere Reserve and World Heritage Site, the most biologically diverse site under UNESCO protection. We should never forget that these rugged islands and coastal deserts contrasting with the surrounding turquoise waters are not only strikingly beautiful but an irreplaceable part of our shared world.

See also
Guadalupe Canyon Hot Springs - The Most Unique Camping in Baja

La Paz is a natural departure port for boutique cruises. We traveled on a scenic bus transfer from San Jose De Cabos to La Paz, where we boarded the Safari Voyager at the Muelle Fiscal pier in downtown La Paz. I saw 30 or 40 humpback whales from my bus seat, which was a good day of whale watching by any measure!

Pro Tip: We wrote a full UnCruise review of the Safari Voyager if you’d like to learn more about the boat and its crew

La Paz Mexico via Canva
La Paz at night

Isla Espiritu Santo / Isla Partida / Los Islotes

A series of islands sit five miles off the mainland outside of La Paz, including Isla Espiritu Santo, Isla Partida, and Los Islotes. Isla Espiritu Santo is the largest island, with 31 sq mi of land and hills rising to 1,844 ft. 31.183 sq mi). It’s a beautiful world of contrasts with white sandy beaches, crystal clear aquamarine waters, and sheer rocky bluffs. It’s exceptionally biologically and ecologically diverse and precariously close to a rapidly developing city.

Espiritu Santo is the only known habitat of the black jackrabbit and Espiritu Santo antelope squirrel. It was slated to have a resort casino until a coalition of conservation-minded eco-adventurers raised funds to purchase and protect the land for future generations. There are several layers of designation and protection for this region, including:

  • Islas del Golfo de California Flora and Fauna Protection Area (APFF-IGC)
  • Archipiélago Espíritu Santo National Park
  • UNESCO Biosphere Reserve
  • UNESCO World Heritage Site

One of the biggest draws for the archipelago is a sea lion nursery on Los Islotes dubbed La Lobera, the Wolf’s Den. Baby sea lions are known as the puppies of the sea because they love to interact with snorkelers by grabbing their fins and doing tricks. Ensenada Grande beach, on Isla Partida, was voted the most beautiful beach in Mexico by The Travel Magazine, and the El Cardonal Trail takes you by some of the largest cacti in the world. Sea kayaking around the chain of bays is a popular activity, which you can do right from boutique cruises or as a multi-day glamping trip from the mainland.

This area can be reached by small boats leaving from the cruise port, but that shore excursion isn’t currently offered. Boutique cruises sail out from La Paz and explore the archipelago for a day or two. The anchorages around the islands are particularly sheltered, so much so that they are part of the emergency response plan for the Pichilingue Cruise Port in case of extreme weather. Small ship captains can modify the trip’s itinerary for the safety and comfort of the guests. We spent an extra night in a sheltered cove off Isla Partida, exploring the beaches, hills, and arroyos, waiting for the weather to clear.

Snorkeling with Sea Lions Los Islotes Baja Mexico- Sea arch by the nursery
UnCruise Snorkeling w- Sea Lions Los Islotes Baja Mexico- Isn't he a playful fellow
El Cardonal hike Isla Partida Baja Mexico

Isla San Francisco

Isla San Francisco is about 20 miles northwest of the Espiritu Santo Archipelago. It’s a popular destination for small boats because of an exquisite crescent-shaped bay on its southern tip that forms a natural anchorage called Half Moon Bay. Populr activities include snorkeling, kayaking, and SUPing in the bay and exploring the mile-long beach. However, the hike to the Mirador de la Isla San Francisco overlook is worth it. Perhaps more of a scramble across rock flats than a proper hiking trail, but you’re rewarded with a postcard view of Half Moon Bay.

Isla San Francisco is too far for shore excursions from La Paz, but it’s an ideal destination for boutique adventure cruises. Small cruise boats under 100 people can anchor in the bay and offer guests a full day of adventure, including happy hour beach parties.

Panorama of Isla San Francisco via UnCruise
Hiking on Isla San Francisco via UnCruise
Guests hiking in Isla San Francisco via UnCruise

San Evaristo / Isla San José

A little farther up the Baja coast sits Isla San José, the region’s largest island and the 6th largest island in Mexico. It measures just under 20 miles tip-to-tip. It’s a rugged, remote wilderness highlighted by crystal blue water and an arid desert landscape. San Evaristo is a sleepy little town across from Isla San Jose on the mainland.

Boutique cruises offer the usual menu of activities here: hiking, SUPing, snorkeling, and skiff tours, but pay special attention to the kayak options around Isla San José. On the island’s south end, you’ll find a sand spit covered by a dense mangrove forest. If the tides are right, you can penetrate the tidal basin and explore a remarkable estuary filled with live and vibrant green colors. On the island’s north end, here’s a series of sea arches you can paddle through as you navigate sheer sea cliffs dotted with hidden beaches.

See also
11 Romantic Places to Eat and Things To Do In Seattle Southside
Snorkeling off Isla San Jose Baja Mexico
Kayaking off Isla San Jose Baja Mexico

Bahia Agua Verde

Bahia Agua Verde is the next port of call up the coast for boutique Sea of Cortez cruises. It’s a cherished stop for UnCruise because of their close relationship with the Romero family, local rancheros who bring their mules down to Agua Verde for guided trail rides through the hills. Other highlights include paddling the bay to Roca Solitaria, a rock pillar that “guards” the entrance to the bay and home to many blue-footed b00bies.

Bahia Agua Verde Mule Ride
Bahia Agua Verde Beach Party
Kayaking in Agua Verde - Via UnCruise
Kayaking in Agua Verde - Via UnCruise

Puerto Escondido

Puerto Escondido is another iconic stop for Baja adventure cruises. Not just because it’s a superior anchorage, but it’s the launch point for an epic overland adventure to the gray whale birthing lagoons. Eastern Gray Whales travel over 2,500 miles yearly to one of three birthing lagoons on the Baja’s pacific coast for the winter.

Whale-watching tours in these lagoons differ from anything else you’ve ever experienced. Instead of chasing the whales as they’re cruising up and down the coast, you putter around the bays in 15-person pongas and let the whales come to you. The whales’ spy hop, fluke splash, and sometimes even approach the boats close enough to look into their eyes and imagine what wonders they have seen.

It’s a full-day Baja road trip adventure over the mountains and across the peninsula to see the whales, but you might have enough time in the evening to take a sunset nature cruise before enjoying a quiet night in a safe harbor.

Grey Whales in Magdalena Bay
Guests experience gray whales Magdalena bay via UnCruise
The coastline of Baja via UnCruise
Kayaking in Puerto Escondido via UnCruise

Loreto

Loreto is the northernmost port of call for Sea of Cortez cruises. Mega cruise ships use tenders to reach the town, and sometimes boutique cruises will use bus shuttles to travel up the coast from Puerto Escondido.

Loreto was once the capital of all of California and California Sur. Its rich history hasn’t been spoiled by modern development and is still visible in the town square and 300-year-old mission and readily accessible to walking tours. Small boats travel out to Isla Coronado, where white sand beaches stretch to crystal-clear turquoise water. These will seem remarkably beautiful and natural if you’re on a mega cruise and overcrowded if you’re coming off a boutique cruise.

Loreto town mexico
Loreto town mexico
Malecón de Loreto
Loreto Municipal Building artwork

Final Thoughts on Sea of Cortez Cruises

There are definitely two distinct styles of cruising the Sea of Cortez. Traditional mega cruises travel farther and faster with highly curated and synthesized shore excursions. Boutique cruises stay closer to shore and travel through the protected islands and coastlines.

Almost half a million people take traditional cruises from Baja and the Gulf of California annually, sometimes even sailing from San Diego and Los Angeles. But, if you love adventure and desire a deeper experience in a natural wonderland, you’d want to travel less and see more on a small-ship adventure cruise. You can always add time to the front and back end of your trip in Cabo for traditional shore excursions or additional adventures like scuba diving the drop-offs and sea mounts just off Cabo’s shore with a good chance of seeing sharks and other pelagics.

Decided a boutique small-ship cruise is for you?? Good news, we have a special gift for you🎉
Use the code Coleman500 for $500 off any UnCruise destination throughout the year‼️ 
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Disclosure: A big thank you to UnCruise for hosting us, and usage of some of the images throughout (image credit in hover text 😉)! For more travel inspiration check out their InstagramFacebookTwitter, and YouTube accounts.

As always, the views and opinions expressed are entirely our own, and we only recommend brands and destinations that we 100% stand behind.

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Bahia Agua Verde beach with kayaks
Sea of Cortez sunset
Baja California Sur coastline
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