Ultimate Baja Mexico Cruise: The Sea of Cortez with UnCruise

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From the moment we were first introduced to the company, we knew we wanted to take a Baja Mexico cruise on the Sea of Cortez with UnCruise Adventures.

Truth be told, this is a part of the world that very few travelers actually venture to. I know that may be hard to realize, seeing as the southern tip of the Baja Peninsula is home to the famous resort towns of Cabo San Lucas and San Jose del Cabo.

Despite that, few people venture north the sleepy town of La Paz, let alone farther north to explore unreal islands and coastlines. It’s just not the thing to do.

This makes the 8 days you spend exploring the region on a small expedition ship a bit unreal.

The days are spent whale watching from the bow, kayaking in crystalline waters, hiking among towering cactus, snorkeling over reefs and bird watching from the edge of a skiff.

It’s untouched. It’s paradise. It’s the UnCruise Adventures way.

UnCruise Adventures in the Sea of Cortez

The Sea of Cortez UnCruise Experience

UnCruise Adventures is the company that was made for people that don’t enjoy standard cruising. Their itineraries are built around nature and you’ll find standard port calls to be on the elusive side with them.

Their itinerary is designed to immerse you into the destination, exploring and learning about the area. We got up close with the wildlife, islands, coastlines, and desert in a way that few other companies can deliver.

This is all done from the comfort of the beautiful Safari Endeavor. The fanciest ship in the UnCruise fleet, you sail with not more than 120 other guests.

Despite it being an expedition ship, which generally gives you more standard accommodation, the Endeavor is a very comfortable base ship. The cabins are spacious for a small ship and all offer a private bathroom, closet, desk, and window.

The food is really special since UnCruise cultivates local relationships and then tailors their menu to serve Mexican specialties.

Multiple activities are offered daily, meaning you can pick and choose based on your fitness levels and interests.

Round this out with a huge, comfortable lounge, open bar, nightly educational presentations about the area, hot tubs, a fitness space on the top deck and you have the perfect environment for an unforgettable trip.

The best part? Sailing with UnCruise is all-inclusive. You pay before you come and once you are on board, everything is included. Food, drinks, and activities are part of the experience.

They specialize in getting people into destinations and having them experience it with a nature first mentality. In the Sea of Cortez, they are one of less than a handful of ships that sail into the Loreto National Marine Reserve.

Sunset while cruising the Sea of Cortez in Mexico

Arrival into San Jose del Cabo

Most people that wish to take a Sea of Cortez cruise will find themselves arriving into the major hub at San Jose del Cabo. Alternatively, you can fly into La Paz, but it is a much smaller airport with fewer flights scheduled. It is also much more expensive.

Like the masses, we chose to access the area through the larger hub in San Jose del Cabo. The international terminal is modern and easy to navigate.

If you are arriving at the start of your Sea of Cortez cruise, your transportation will be arranged to get you to La Paz, where you will join the boat.

While the company waits for the arrivals, you will be brought to the UnCruise partner hotel, the Barcelo Gran Faro. Here they have a comfortable hospitality area set up and it is possible to get an access bracelet for the property if you are arriving early.

The transfer to La Paz leaves the Barcelo Gran Faro at 3 pm. The drive takes around 3 hours to reach the central pier in La Paz from San Jose del Cabo.

If you plan to arrive a few days before the start of the cruise, you will need to book your own transportation to your hotel in San Jose del Cabo, Los Cabos or book a transfer up to La Paz.

With winter in Wisconsin being, well, winter, we opted to fly in a few days early and head straight up to La Paz to acclimatize and do a kayaking expedition on Isla Espirito Santo before joining UnCruise to cruise the Sea of Cortez.

We booked our transfer with Eco Baja Tours and the process was seamless. It is possible to book tickets online, which is what we recommend, but if you want to change it, you can show up and buy tickets at the airport too.

The transfer takes 3-4 hours, depending on which route you book. Both will get you where you are going, but having done both routes, I’d recommend booking the transfer that takes you via Todos Santos and avoids the mountains.

We ended up booking the other route that goes via Los Barilles and not only did it take longer but crossing the mountains was slow. Plus, if you’re prone to motion sickness, this route is a bit hairy.

UnCruise docked in La Paz Mexico

Cruising from La Paz

David and I took our first trip to Mexico together in 2003. We went to Playa del Carmen and at that time, it was still very much a small town. Over the years we’ve watched it change and morph into the megacity it is today.

When we arrived in La Paz, we were instantly flashed back our first visit to Playa del Carmen. Tourism and major development have not arrived in La Paz, yet.  When you walk the streets, you’re met by locals and expats.

There are no mega-hotels or souvenir shops and the whole town gives you a feeling of really being in Mexico.

It’s the perfect place to spend a few days adjusting to the weather and adventuring before heading off to cruise the Sea of Cortez.

Something worth noting, if you have your heart on seeing whale sharks, you will want to arrive at least a day early to La Paz and book a whale shark tour.

The UnCruise itinerary does not include any activities to see the whale sharks in the Sea of Cortez.

When the embarkation day arrives, you will be able to board the Safari Endeavor at 6 pm. You will want to be a bit early to the pier to beat the bus that is arriving from San Jose del Cabo.

Once that bus arrives and all passengers are on board, the ship leaves La Paz.

With this in mind, if you want to spend some time exploring La Paz and the surrounding area, you should fly in early and spend a few nights.

Read more 32 Awesome Things to Do in La Paz, Mexico


Our Sea of Cortez Cruise Stops

The biggest thing I want to communicate is that no two UnCruise itineraries are the same. This is on purpose and all part of the adventure. Every expedition is dictated by weather and wildlife, meaning it is impossible to guarantee a certain set of stops.

As a disclaimer, I cannot guarantee that if you take this cruise that you will make these same stops. UnCruise has permits to visit a wide range of islands, bays, and areas within the Sea of Cortez for their cruises.

That said, you can expect that every stop will be spectacular. This was our third time cruising with UnCruise, we’ve previously done the Inside Passage of Alaska, Costa Rica & Panama) and they have amazing adventure itineraries down to a science.

Isla Monserrat in the Sea of Cortez Baja Mexico

Isla Monserrat

Located in the heart of the Loreto National Marine Reserve, Isla Monserrat was our first stop of the week.  This was an island that wasn’t on our radar and according to the crew, a place that is rarely visited because of the way the wind acts around this island.

It is not often accessible due to large waves and rough seas, however, we had luck on our side and the easing of winds after the full moon that made it possible for us to stop.

Mirroring the excitement from the crew, we weren’t sure what to expect so we opted to sign up for a hike that would get us up close and personal with a large spread of towering yellow rocks along the beach.

Adequately named, Yellowstone Beach delivered stunning landscapes and a brilliant introduction into the vast diversity of the area.

Our skiff dropped us at one end of the beach, and we spent 2 hours beachcombing, climbing yellow rock and making our way to the opposite end of the beach where we discovered huge tide pools among rough rock that was covered with skittish Sally Lightfoot Crabs.

Pilot Whales in the Sea of Cortez - Loreto National Marine Park
Pilot Whales are seen from our UnCruise Adventures ship

Loreto National Marine Reserve

I am going to just come right out and say it. The Sea of Cortez is a superb place for whale watching. Especially within the Loreto National Marine Reserve, a place that several species of whale call home during the winter month in the Northern hemisphere.

Of the 8 days we spent with UnCruise, 6 days were spent sailing around the Loreto National Marine Reserve. Taking a Baja Mexico cruise is an amazing way to go whale watching.

We spotted marine mammals daily with some of our best sighting including Blue Whales, Fin Whales, Bottle Nose Dolphins, Common Dolphins and a massive pod of Pilot Whales.

Birdwatching in Agua Verde Mexico

Bird Watching in Agua Verde

Located on the peninsula, Agua Verde is a sleepy little fishing village that opens its bay to UnCruise during the winter months. Setting anchor in the bay, we were offered a variety of activities throughout the day.

For us, we went all in and signed up for three activities. It meant we would be busy, but we had the weather on our side, and we wanted to explore all that was on offer.

This meant we were up early and off the ship before 7 am to do some land-based bird watching. This is a special activity in a place like Baja because most of the bird watching you do is sea-based.

Having the chance to head into a lush area on foot meant we would get a close up look at land birds you would never see from the water. It didn’t disappoint and we easily logged 13 species over 2 hours including the endemic Costa’s Hummingbird, Vermillion Flycatcher, Phainopepla, Hooded Oriole, endemic Grey Thrasher and Northern Mockingbird.

Blue Footed Boobies in the Sea of Cortez - Baja Mexico cruise

Skiff Tour Around Bahia Agua Verde

After spending our morning on land, we hopped on a skiff tour to look for sea birds. Just off the beach in Bahia Agua Verde are two spectacular rock formations. One further out, just on the edge of where the bay meets the ocean, meaning it is more exposed and closer to the beach.

It was here that we would enjoy spotting several blue footed boobies! Admittedly, February is a bit early for spotting boobies, but we got lucky. We also saw a couple of brown boobies too.

Additionally, we enjoyed seeing large quantities of pelicans, gulls and cormorants along the rocky outcrops. We even got lucky and spotted two osprey nests along the coast in our explorations.

The peninsular coast and islands that dot the Sea of Cortez are known as the Galapagos of the North and after our visit, I can attest to this.

Burro Riding at Bahia Agua Verde Mexico

Burro Ride with the Romero Family

After lunch, we loaded up on the skiff and headed off to shore for another land-based activity. This would be a one-hour burro ride around the area to check out the diversity in the land and take in some spectacular views from above.

UnCruise has a beautiful relationship with the local Romero family, who owns a large herd of well-behaved burros and mules. They have been riding through the lands of Agua Verde for several generations and continue the tradition today.

Whenever UnCruise is coming to port in Agua Verde, the Romero family brings a team of their best burros to the beach.

Our ride was a highlight of the itinerary, taking us up the steep slopes of the island to view the stunning bay from above.

Descending on the far side we rode through the desert and into a passive riverbed area that supports a dense forest of plants with minimal water.

Leaving the lushness of the riverbed we headed out along the coast and then back up again before descending down to more spectacular views of Bahia Agua Verde.

David Stock hiking at Puerto Los Gatos Mexico

Puerto Los Gatos

Waking up the next morning we found ourselves at anchor off the shores of a place that was in stark contrast to the place we had explored the day before.

Even from the ship, the bright red rocks of Puerto Los Gatos told us we’d be having another up-close look at the amazing diversity in this part of the world.

This day we opted for an exploratory hike, one of the flagship activities of the UnCruise model, a way to get up close and dirty with the destination.

Leaving the ship in a small group, we were brought to shore on the skiff. Here we were briefed by our expedition leader before heading off to explore the bright red rocks and head off into the lush desert.

The goal of most exploratory hikes is to gain elevation and get amazing views. This is, of course, more of a challenge when you have a desert to navigate.

Everything in the desert is designed for survival, meaning it bites or sports spikey exterior to protect itself. This makes ‘bush-whacking’ a bit of a challenge.

Hikes like this are slow-moving, yet strategic. Our group managed to traverse along a hill before following a rock slide up to the top of the hill. The panoramic view really gave us a sense of how beautiful the desert can be when it has been given rain.

Coming down, we followed a path into an open expanse of grazing land before heading back past several massive cardon cactuses and back onto the beach.

Grey Whale in Magdalena Bay Mexico

Magdalena Bay

From mid-January to late March, UnCruise alters their normal Sea of Cortez Baja cruise itineraries to include a day trip to the Pacific Coast and Magdalena Bay.

Every year, large numbers of grey whales make the migration south to the protected Magdalena Bay where they calf. They then remain for several months to raise the calves before starting the migration north again for the summer.

This means you have the opportunity for some very intimate whale watching in this part of the world.

I’d be lying if I said we didn’t specifically time our itinerary for this opportunity! We totally did and it didn’t disappoint.

The drive across the Baja peninsula takes around 3 hours and once you arrive in the sleepy Pacific town of Puerto Aldolfo Lopez Mateos, you are whisked right off the start 2 hours of whale watching in Magdalena Bay.

Two words, simply amazing. This is one of the most intimate and special wildlife experiences we have ever had.  Over the span of an hour, we saw several dozen whales and calves.

They are also extremely curious and even approach the small boats. We witnessed breaching, pectoral slapping, spy hopping and more just feet from us.

If you have the flexibility to plan your Baja cruise during these months, do it!

Sea Lion at Los Islotes, Sea of Cortez Mexico

Los Islotes

High on our amazing grey whale experience from the day before, the next stop on our itinerary would be off the coast of the UNESCO World Heritage-listed Isla Partida at Los Islotes. This is easily a highlight of any Baja Mexico cruise.

Located here is one of the largest sea lion rookeries in the world. Taking the title of the southernmost rookery for the California sea lion, it is a place where you have the chance to get right in the water with these playful critters.

They are playful and are used to having both researchers and tourists snorkel in the waters near them. The young ones are very playful and even approach you while you swim along.

After having the chance to swim with sea lions repeatedly in the Galapagos Islands, we were not passing up the chance to do it at Los Islotes too.

Ensenada Grande on Isla Partida Baja Mexico
Ensenada Grande on Isla Partida

Isla Partida

In the afternoon, we were offered a variety of options at the famous Ensenada Grande. We could choose between hiking, kayaking, snorkeling and skiff tours to explore the area.

Before we joined UnCruise, we took a 4-day kayaking and camping trip along Isla Partida and Isla Espirito Santo. It just so happened that our first campsite on that trip was actually at Ensenada Grande, so we had already done most of the activities on offer.

With this situation, we opted for a skiff tour to explore the coastal areas a bit more. Turns out, with the beautiful weather, everyone opted for the other activities and we were treated to our own private skiff tour that afternoon!

We covered a lot of distance and explored coastal areas we didn’t get to see on our kayaking trip. The highlight was hands down coming across a massive osprey nest and then witnessing one of the birds fly in with a huge fish for its mate.

These are moments that we travel for, the wild unpredictable ones. The kind of moments that are made possible when you choose to travel with companies like UnCruise Adventures.

Read more: Isla Espiritu Santo in Mexico: Ultimate Planning Guide

Isla San Franciso in the Sea of Cortez Mexico

Isla San Francisco

A week really flies by when you’re having fun and in the blink of an eye, we were waking up at our last stop.  This day would give us an amazing look at one of the most beautiful islands in the Sea of Cortez, the stunning Isla San Francisco.

This island is known for its amazing bay and dramatic topography, so our goal was to get up high and take it all in.

UnCruise offered 3 hiking options that morning and while we considered doing the classic ridge hike, we decided we wanted a bit more intensity and signed up for the more aggressive climb.

It was the right decision for us! Our morning was spent doing an aggressive hike to the highest point of the island. From here we had a full 360-degree view of the surrounding islands and ocean.

Although we couldn’t really see the classic overview of the crescent bay that the island is famous for, it felt like being on the roof of the world. We could even see whales spouting in the distance from that vantage point.

Knowing we wanted to get the classic view, we began a descent from the highest peak and skirted around another peak to the other side of the island. Here we followed a wash line down until we met up with another peak and began to climb up again.

Reaching the top of this peak gave us incredible views of the famous bay below. We stood in awe for the better part of 30 minutes, taking it all in and grabbing photos from the giant boulders that lined the ridge.

We then began descending down along a trail into a salt pan that separates the beach on the bay and the opposite side. Crossing the salt pan, we arrived back on the beach with a clear view of the mother ship.

We were taken back on board for lunch and the afternoon was spent as an open beach day, meaning we could partake in SUP, kayaking, snorkeling, swimming or beach lounging for the rest of the day.

UnCruise does these things right, setting up a beach bar, offering up shade, chairs and just letting people enjoy their time in paradise. Needless to say, it was the perfect ending to an amazing week.

Back to Reality

All good things must come to an end and no truer words could be spoken for a trip like this one. Sailing back to La Paz and to reality was a bit jarring, to be honest.

We have walked away from our Baja Mexico cruise around the Sea of Cortez knowing that it will easily be one of our favorite expeditions for a long time. 

Barcelo Gran Faro in Los Cabos Mexico
Pool at Barcelo Gran Faro in San jose del Cabo

Staying in San Jose del Cabo

After having an experience like cruising the Sea of Cortez, we’d recommend that you also add a few nights after the trip in either La Paz or Cabo. Seeing as we came down early and spent time in La Paz, we opted for a post-trip stay in Cabo. 

UnCruise books people into the beachside Barcelo Gran Faro, but you could also book any other properties in the area if the all-inclusive beach resort vibe isn’t really your scene. 

That said, we found the Barcelo Gran Faro to be very comfortable. The grounds are beautiful and the pools are nice. They also have a beautiful beach area and plenty of chairs for all the resort guests. 


Complete Baja Mexico Cruise Itinerary 

Baja Mexico cruise itinerary

We sailed on the itinerary called Baja’s Bounty. The cruise includes transfers from and back to the San Jose del Cabo airport. That said, the ship docks in La Paz, about three hours north of Cabo.

I want to reiterate that we are including our specific itinerary below. However, you need to know that this is not a set itinerary. Every trip is different based on weather and sea conditions. 

There are no guarantees that you will visit all of the same places that we did. But don’t worry about that. Everything in the Sea of Cortez is amazing and you cannot go wrong with any of the islands. 

  • DAY 1: Arrival in San Jose del Cabo and transfer to La Paz – Embarkation
  • DAY 2: Isla Monserrat, Loreto National Marine Reserve
  • DAY 3: Bahia Agua Verde
  • DAY 4: Puerto Los Gatos
  • DAY 5: Magdalena Bay – Pacific side of Baja Peninsula
  • DAY 6: Los Islotes and Isla Partida
  • DAY 7: Isla San Francisco
  • DAY 8: Arrival in La Paz and transfer to San Jose del Cabo – Disembarkation
UnCruise Adventures in the Sea of Cortez - Baja Mexico Cruise

How to Take a Sea of Cortez Cruise with UnCruise

UnCruise Adventures is a small company headquartered in Seattle, Washington. They operate itineraries in Alaska, Pacific Northwest, Columbia & Snake Rivers, Mexico, Central America, Galapagos, and Hawaii. You can book directly with UnCruise to cruise Mexico on this amazing itinerary.

You can book our same itinerary here: Baja’s Bounty  Be sure to tell them that Divergent Travelers sent you!

More on UnCruise:

More on Mexico:

We partnered with UnCruise Adventures to bring you this story. All opinions, photos, stories and insane love for ‘uncruising’ are 100% our own. As always. 

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Cruising The Sea of Cortez Pinterest Pin


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About Lina Stock

Lina is an award-winning photographer and writer that has been exploring the world since 2001. She has traveled to 100 countries on all 7 continents. Member: SATW, NATJA, ATTA, ITWA



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