A Sea of Cortez Cruise is a great way to see “the world’s largest aquarium” as Jacques Cousteau called it. This is a paradise for nature lovers, as it contains one-third of all marine mammals on Earth, along with 900 bird species, crystal clear water and white sandy beaches.
This article includes interactive maps, a focus on shore trips and information on the ports-of-call and overnight anchorages that you will find on a Baja Mexico Cruise for mega cruise ships or smaller boutique adventure cruises. If you’ve ever wanted to follow in the footsteps Steinbeck and Cousteau, or explore one of the world’s most diverse biomes, then keep reading.
Cabo San Lucas
Cabo San Lucas is the starting point for many Baja Mexico Cruises, thanks to its large cruise port and Los Cabos International Airport. Direct round-trip tickets costing less that $200 from several US cities and taking less than three hours to fly are also available.
You’ll be responsible for the 30-mile transfer ($60), and possibly a hotel night, if you’re taking a mega-cruise. UnCruise, a boutique cruise brand, does things differently. They partner with a hotel near the airport and package in airport shuttles.
Cabo, Mazatlan, and Puerto Vallarta are part of a cruise triangle that has existed for many decades. This area is home to a vibrant shore excursion business. From the harbor depart a variety of boat tours, from romantic sails to kid-friendly pirate ships. All boats, no matter what flavor they are, pass the famous Cabo arch which is located just outside of the harbor. They then go to Lover’s Beach (near the Arch) or to other beaches, such as Playa Santa Maria and Chileno Bay where they can swim or snorkel. They sometimes cruise the coast in search of whales and dolphins.
Adventure parks like Wild Canyon Adventures or Canopy Costa Azul offer ziplines, rappelling, and ATV tours.
San Jose del Cabo
Boutique cruises, like our Baja UnCruise cruises, use Cabo’s developed infrastructure in a different way than mega cruises. The Barcelo Grand Faro Los Cabos is the resort they have chosen to use for the staging of the cruise before and after it. This has been included in the price.
I was met by a shuttle bus at the airport that took me straight to the resort. On the day of arrival, we stayed the night at the resort, which included buffets, swimming pools and a private sandy beach. On the day of departure, we returned mid-morning to the resort. Many people on my cruise booked their flights to coincide with the resort days, so that they could enjoy off-property activities. The concierge desk at Barcelo can arrange for activities like adventure parks or you can take an Uber to downtown San Jose del Cabo and enjoy some Mexican culture.
Mazatlan
Remember the “Cruise Triangle” between Cabo, Mazatlan and Puerto Vallarta? The rub. The problem is that two of these ports (Mazatlan, and Puerto Vallarta), are not in the Gulf of Mexico nor the Baja. These ports are located on the Mexican Riviera, which is part of the Mexican mainland. It’s not good news that the ocean floor drops rapidly outside Cabo to 1200 feet. 90% of the fish in “the World’s Aquarium”, live above the continental shelf. They are on many mega cruises, but we will cover them here. You’ll also get to experience the tropical jungles, as well as different indigenous influences such Papantla Flyers.
Mazatlan has a population of half a million and is over 500 years old. You can choose from a variety of tours, including hiking up to the Faro Mazatlan lighthouse on a hill above the port, or venturing into the city to visit the Plaza Machado and Malecon de Mazatlan. The only other option is a Stone Island beach excursion, which was the least-rated. You’ll find more beautiful beaches at other stops.
A bus tour to the villages Concordia and Copala will allow you to experience the life at the foothills the Sierra Madres. You can see adobe-brick making demonstrations, historic churches, and pottery. There’s also a zip-line option, but the most popular excursion and the one that gets the highest ratings is salsa classes in a nearby resort. Which salsa? Which salsa? You will learn how to cook the traditional Mexican food and dance the Latin dance. This is a great option for those who are unsure of what to do. Its popularity and rating speak volumes about the many things in Mazatlan.
Puerto Vallarta
Puerto Vallarta (or PV) was a sleepy town until American tourists realized how beautiful it is. Although its bay is one of largest on the Pacific Coast and the Port of San Blas was the main port because of the overland routes from Guadalajara.
John Huston’s 1964 film The Night of the Iguana introduced PV to America. Cruise lines were fascinated by the natural beauty of the area, the deep-water port and the undeveloped land. More than 450 000 cruise passengers visit PV each year, and are welcomed with a wide range of shore excursions.
Most popular are the city tours in Puerto Vallarta, where you can see a combination of Elizabeth Taylor’s Gringo Gulch and historic waterfronts, as well as churches and tequila.
Adventure is plentiful in PV. Los Veranos Canopy Tour is allegedly the largest zip-line tour in the entire world. Banning Mills, Georgia, holds the record for the World’s longest zip line canopy tour, with more than 100 lines that travel over 11 miles in the air. Los Veranos offers more than just 19 zip lines through the canopy of the jungle. There are also e-bike and hiking tours as well as river play.
From the port, you can take a variety of beach excursions. These include exclusive beach resort getaways as well as boat tours to remote bays such Playa Majahuitas or Playa Yelapa. You can even snorkel in the waters around Islas Marietas.
La Paz
La Paz has a lower number of mega-cruises than the “Cruise Triangle.” In 2022 it saw 21 cruise ships dock, less than Cabo San Luis does every month. This will change soon as Pichilingue Cruise Port, which has recently expanded, becomes more popular.
There are only a few excursions available, such as scenic drives, shopping and artisans, as well highlights of La Paz like the Cathedral Nuestra Senora de La Paz or Baja California Sur Regional Museum. These experiences could be merged and expanded to include whale shark watching and snorkeling with baby seal lions in the nursery at Los Islotes.
The impact of La Paz’s cruise port on the environment could permanently alter a natural sanctuary or be a window into the world, where people can learn about and practice ecotourism. Currently, 244 Islands and Protected Areas of Gulf of California UNESCO Biosphere Reserve, World Heritage Site are the most biodiverse site under UNESCO’s protection. These rugged islands, coastal deserts and turquoise waters surrounding them are not only beautiful but also irreplaceable.
La Paz is a natural departure port for boutique cruises. We took a scenic bus from San Jose De Cabos up to La Paz where we boarded Safari Voyager on the Muelle Fiscal Pier in downtown La Paz. I saw between 30 and 40 humpbacks from the bus, which is a great whale-watching day by any standard!
Isla Espiritu Santo / Isla Partida / Los Islotes
Isla Espiritu Santo is the largest island, with 31 sq mi of land and hills rising to 1,844 ft. Isla Espiritu Santo has the most land, covering 31 square miles and rising to 1,844 feet. The island is a world of contrasts, with its white sand beaches, aquamarine water, and sheer rocky bluffs. The area is incredibly diverse in terms of its biological and ecological diversity, and it’s located dangerously close to a rapidly growing city.
Espiritu Santo has been identified as the only habitat for the black jackrabbit, and Espiritu Santo squirrel. The land was originally slated for a casino resort until a group of eco-adventurers who are committed to conservation raised money to buy and protect it. This region is protected in several ways, including:
- Islas del Golfo de California Flora and Fauna Protection Area (APFF-IGC)
- Archipielago Espiritu Santo National Park
- UNESCO Biosphere Reserve
- UNESCO World Heritage Site
The sea lion nursery, La Lobera (the Wolf’s Den), on Los Islotes is one of the most popular attractions in the archipelago. The baby sea lions, also known as puppies of the ocean, love to play with snorkelers and grab their fins. The Travel Magazine voted Ensenada Grande Beach, on Isla Partida as the most beautiful beach of Mexico. The El Cardonal Trail leads you past some of the biggest cacti around. You can go sea kayaking in the bays from the boutique cruises, or on a multi-day trip from the mainland.
This area is accessible by small boats departing from the port of departure, but this shore excursion has not been offered yet. Boutique cruises depart from La Paz to explore the archipelago. Anchorages are so sheltered around the islands that they form part of an emergency response plan in the event of severe weather. The captains of small ships can change the itinerary to ensure the safety and comfort for their guests. We stayed an extra night at a cove near Isla Partida to explore the beaches, hills and arroyos while we waited for the weather.
Isla San Francisco
Isla San Francisco lies about 20 miles north of the Espiritu Santo archipelago. Half Moon Bay, a crescent-shaped natural anchorage on the southern tip of Isla San Francisco, is a popular destination among small boats. Popular activities include kayaking and SUPing on the bay, as well as exploring the mile-long sandy beach. The hike to the Mirador of la Isla de San Francisco is well worth it. The trail is more like a scramble over rock flats, than a hiking trail. But you are rewarded with a picture-perfect view of Half Moon Bay.
Isla San Francisco, though too far to reach by shore excursion from La Paz is a great destination for boutique adventure ships. Small cruise boats with fewer than 100 passengers can anchor in the bay to offer a full-day of adventure and beach parties.
San Evaristo / Isla San Jose
Isla San Jose is the largest island of the Baja region and the sixth largest in Mexico. The island is just over 20 miles long from tip to tip. This rugged wilderness is characterized by arid landscapes and crystal-clear water. San Evaristo, a sleepy town on the mainland across from Isla San José, is a remote wilderness.
There are a variety of activities available on boutique cruises, including hiking, SUPing and snorkeling. Pay special attention to kayaking options in the area around Isla San Jose. You’ll find dense mangrove forests on the south end of the island. You can explore the estuary and its vibrant colors if the tides are just right. You can navigate the sheer sea cliffs and hidden beaches on the north side of the island by paddling through a series sea arches.
Bahia Agua Verde
Bahia Agua Verde, the next stop on the boutique Sea of Cortez Cruises up the coast is Bahia Agua Verde. UnCruise is a fan of this stop because they have a close relationship with local rancheros, who bring their mules to Agua verde for guided trails through the hills. Paddling to Roca solitaria is another highlight. This rock pillar guards the entrance of the bay, and is home to blue-footed b00bies.
Puerto Escondido
Puerto Escondido, another Baja adventure cruise stop, is a must-see. It’s not just a great anchorage; it’s also the starting point of an epic overland journey to the gray-whale birthing lagoons. Eastern Gray Whales migrate over 2,500 miles each year to one of the three birthing lagunas along the Baja pacific coastline for the winter.
Whale watching tours are unlike anything you have ever done before. You don’t chase the whales up and down coasts, but rather cruise around the bays with 15-person pongas. The whales will come to you. Whales will spy hop and fluke splash and even come up to the boats so close that you can look into their eyes.
You can enjoy a sunset cruise in the evening before spending the night in a quiet harbor.
Loreto
Loreto is the most northern port of call on Sea of Cortez Cruises. Mega cruise ships will often use tenders in order to reach Loreto, while boutique cruises may use shuttle buses to travel from Puerto Escondido up the coast.
Loreto used to be the capital city of California Sur and all of California. The rich history of Loreto has not been altered by modern development. It is visible in the 300-year old mission, as well as on the town square. Walking tours are available. Isla Coronado is a small island with white sands and turquoise waters. Small boats take you there. If you are on a mega-cruise, these will appear beautiful and natural. However, if you have just returned from a boutique cruise they may seem overcrowded.
Last Thoughts about Sea of Cortez Cruises
There are two distinct styles of cruising on the Sea of Cortez. Mega cruises are more traditional and travel faster, with a curated itinerary of shore excursions. Boutique cruises travel closer to the shoreline and through protected islands and coastlines.
Every year, almost half a million people sail from Baja or the Gulf of California. Sometimes they even leave from San Diego or Los Angeles. If you are looking for a more immersive experience and want to see more of a natural paradise, then a small ship adventure cruise is the way to go. It is possible to add extra time in Cabo at the beginning and end of your vacation for shore excursions and additional adventures, such as scuba diving off the coast of Cabo and the seamounts. You may also see sharks or other pelagics.