Whale Sharks & Remote Islands: An Expedition into the Sea of Cortez
Expedition deep into the Sea of Cortez, from La Paz to Bahía de Los Ángeles
Tucked between the Baja California Peninsula and mainland Mexico, the Sea of Cortez is one of the most biologically rich stretches of ocean on the planet. Most visitors explore the south — but the real magic happens further north, where the water is quieter, the islands are untouched, and the wildlife encounters feel like they belong to you alone.
You’ll sail from La Paz northward through rarely visited corners of the Sea of Cortez, stopping each day for snorkeling, kayaking, paddleboarding, and island exploration. Snorkel with sea lions at Las Ánimas — and if luck is on your side, spot hammerhead sharks.
A rare landing on Isla San Pedro Mártir, the most remote island in the Sea of Cortez and home to the world’s largest colony of blue-footed boobies. Reefs that few have ever visited, and if the ocean plays along, finback whales, sperm whales, orcas, and pilot whales.
The undisputed highlight is swimming with whale sharks in Bahía de Los Ángeles — a protected marine reserve hidden deep in the northern Sea of Cortez and home to one of the largest gatherings of whale sharks in the world. Between May and November, up to 220 individuals have been recorded in a single season. With almost no other boats around, it often feels like you have the entire bay to yourselves.
Your ship transits overnight to position you perfectly for each morning’s activities, so every day begins somewhere new. Days are spent in the water and exploring remote islands — snorkeling, freediving, kayaking, paddleboarding — guided by naturalists who bring depth to every experience. This is a small ship cruise built around adventure and exploration — and one of the best opportunities to ethically swim with whale sharks in Mexico.
Whale Sharks & Remote Islands: An Expedition into the Sea of Cortez
Sea of Cortez wildlife — what you might encounter
Isla Las Ánimas punches well above its weight. Beneath the surface, pinnacles and caves draped in sea fans and gorgonians, schooling jacks so thick they block out the light, moray eels, rays, and tuna weaving through it all. A resident colony of California sea lions treats every snorkeler as a personal invitation to play — and from late spring through autumn, hammerhead sharks are drawn to these waters too.
Bahía de Loreto National Park is UNESCO-protected for good reason. Over 800 species of fish patrol its reefs alongside sea turtles, dolphins, and nutrient-rich waters that attract everything from colourful reef fish to passing whales.
Isla San Pedro Mártir is the wildcard. A sheer volcanic rock rising straight out of the ocean, it sits at the meeting point of powerful currents that pour nutrients to the surface — which means the marine life here is extraordinary. Underwater walls drop away into black coral and gorgonian gardens teeming with sea lions, groupers, and seahorses. Above water, the world’s largest colony of blue-footed boobies nests on the cliffs.
Bahía de Los Ángeles is the headline act. One of the largest gatherings of whale sharks in the world assembles here between May and November, drawn in by rich plankton blooms. With almost no other boats in the bay, you’ll slip into the water quietly and swim alongside the biggest fish on the planet — in a protected reserve that feels a million miles from anywhere.
Throughout the journey, keep your eyes on the horizon. Finback whales, sperm whales, orcas, pilot whales, and mega-pods of dolphins all call these waters home.
Respectful marine life encounters
Expert naturalist guides lead all wildlife experiences and operate in full compliance with Mexican marine wildlife regulations — ensuring every encounter is safe, respectful, and deeply memorable.
Our eye in the sky
We collaborate with a year-round research plane over the Sea of Cortez, providing scientists with real-time wildlife observations to support conservation efforts.
Possible wildlife sightings:
- Whale sharks
- Hammerhead sharks
- Schooling fish in huge numbers
- Pilot, fin, & sperm whales (ocassionally)
- Mega pods of dolphins
- Blue-footed boobies and other sea birds
- California sea lions
- Orcas and more!
Snorkeling, kayaking & island exploration in the Sea of Cortez
Every day is shaped by the ocean, the islands, and whatever the conditions have in store — with expert naturalist guides leading the way throughout.
Water temperatures range from the mid-70s to mid-80s°F. It can get seriously hot during the day, so activities are generally scheduled for early morning or late afternoon when the air is cooler — and the boat is fully air conditioned.
Sea of Cortez snorkeling is at the heart of the trip — from sea lion colonies and hammerhead territory at Las Ánimas to the chance to swim with whale sharks in Mexico’s most protected northern bay. The water is warm, clear, and full of life, and you can get in as much or as little activity time as you like.
Kayakers and paddleboarders are well catered for, with a selection of single and double ocean touring kayaks and paddleboards available throughout. Experienced paddlers are welcome to head off independently within safety guidelines, with guided sessions available too.
Ashore, the landscape is just as rewarding — desert hikes through stark volcanic terrain, beach walks, and birdwatching that ranges from seabird colonies on the cliffs to migratory species passing through.
We are also fully permitted to go ashore Isla San Pedro Mártir — a rare privilege.
All water activities are supported by a high-speed RHIB — keeping the group safe, connected, and ready to move the moment something interesting appears on the horizon.
Highlights include:
- Snorkeling & freediving
- Swimming with whale sharks
- Kayaking & paddleboarding
- Hiking & beach walks
- Island exploration
- Birdwatching
Your home at sea



Life on board
These expeditions are based on large ocean-going liveaboard vessels operated by Nautilus Adventures — your home at sea for the week. The daily action happens from smaller, fast support boats designed to get you quickly to the wildlife hotspots, while the mothership handles everything else: comfort, food, and a good night’s rest.
While you sleep, your ship repositions — so every morning you wake up somewhere new, ready for whatever lies ahead. Life on board quickly finds its own rhythm: activities, fresh meals, time to relax, more activities, and then the kind of sleep that only comes after a full day on the water.
Nautilus Adventures is the only liveaboard operator in the world with a certified ISM safety management system — audited annually to the same standards as the world’s largest cruise ships. In short, safety is taken seriously. A full briefing and practice drill on day two means you’ll always know exactly what to do — and can spend the rest of the trip focused on the water.
A Note on Our Partnership
We at Baja Expeditions operate our own naturalist-led group — limited to 8 guests — focused on snorkeling, freediving, and surface activities, with a dedicated fast-boat for our daily excursions. We partner with our sister company Nautilus Adventures, who provides the mothership and also runs a parallel scuba diving group with their own dive guides and fast boat. Both groups travel together on the same vessel exploring the same waters — we simply offer different activity itineraries.
The Nautilus Explorer is a sturdy and well-appointed custom-built 132-foot vessel, designed for comfortable open ocean voyages. She accommodates up to 25 guests across 13 en-suite cabins, ranging from cosy lower deck staterooms to generous suites with large windows — and a premium suite with a lounge and full-size bathtub. All cabins are air-conditioned with private bathrooms.
The main salon and dining room are framed by beautiful large windows with million-dollar views — a great place to unwind, eat well, and watch the stunning Baja scenery go by. The sun deck has plenty of seating for everyone, a freshwater hot tub, and a huge water-level platform that puts you as close to the ocean as you can get without actually being in it.
Explore the Nautilus Explorer- 7 nights’ accommodation on a liveaboard
- Scheduled group transfers
- All core activities and necessary equipment
- All meals and snacks
- Non-alcoholic drinks
- Naturalist guides and expert crew
- Alcoholic beverages and bar
- Gift shop items
- Internet access ($85 per device, per trip)
- Crew gratuities
- Port fee (US$ 35 pp payable in cash onboard)
Your Sea of Cortez expedition itinerary
Please check in at SeeCreatures Cabo by 4:30 pm for your coach transfer to La Paz, where our hosties will be waiting for you on the back deck with trays of margaritas and champagne, dinner on the stove and departure for the Sea of Cortez.
Every day will be different and your captain and dive guides will update your itinerary to maximize animal and snorkeling encounters and minimize any challenges with weather. This is a stunning time of year to explore the Sea of Cortez with water temps typically in the high 70’s and 80s. One of the nicest things about this time of year is that the seas are generally very calm without any motion aboard our heavy steel stabilized ships.
You can expect to visit Las Animas, Isla San Ildefonso, San Pedro Martir, and Bahia de Los Angeles. We will spend the last day at sea exploring our secret hot spot near Mulegé, where pilot whales, dolphins, and other incredible marine life are often encountered.
Morning breakfast. Disembark by 8:00 am with complimentary transfer back to Cabo or SJD international airport. The coach ride can take 2 hours 40 minutes to the airport and for that reason, we recommend booking same day
flights home for 2 pm or later.
Whale Sharks & Remote Islands: An Expedition into the Sea of Cortez
All prices are in US dollars
TRIP DETAILS
WEATHER
The Sea of Cortez is mostly calm this time of year. We will be traversing a lot of areas with regional variations in water temperature and wind. We will likely see water temps ranging from the mid-70s to the mid-80s. It can be very hot during the day, but this is not a problem with air conditioning on board. Comfort on board is ensured, with lots of water activities and shore activities generally scheduled for the first thing in the morning or late in the day when the temperatures are cooler. One of the coolest things about these trips is that, unlike open ocean expeditions, the waters are quite smooth, and there may be very little or no movement on the boat for days at a time.
THE WHALE SHARKS
The whale sharks aggregate in the estuary at the south end of Bahia de Los Angeles, which is a protected reserve in a CONANP national park. Interaction with the whale sharks is by snorkelling only; no diving is allowed. Visibility is typically 30 to 40 feet in the area where the whale sharks gather. Depending on the group’s interest, there will either be a morning session with the whale sharks or two opportunities, morning and afternoon, to get in the water with the animals. We work together with the local dive operator, using his pangas and captains for the actual whale shark interaction. We always reserve our trips with him ahead of time, but this is a small place in the middle of nowhere, and Ricardo and his team are not always available when booked. We always get our guests in the water, but there are sometimes delays.
AIRPLANE SUPPORT
Our team will be in the air at least two days a week during your trip, with constant contact with the ship’s captain. Your pilot and observer enhance the experience by providing insights on the marine environment, with opportunities to encounter finback and sperm whales, solitary whale sharks, orcas if they are in the area, mega pods of dolphins, and much more. Please note that flights are always subject to weather and mechanical limitations.
DIVERS
Approximately 15 dives plus 1 day swimming with whale sharks and hopefully additional snorkelling with cetaceans. A 5mm wetsuit is recommended at the start of the season in July, while a 3mm wetsuit will likely be fine from August onwards. Our SeeCreatures ocean activities centres are located in Cabo San Lucas and La paz are there to support whatever you need from discounted pre-trip adventures including day trips to Cabo Pulmo and Gorda Banks to photography workshops to wetsuit, gear and go-pro rentals. On our Sea of Cortez adventures there’s usually the opportunity for several night dives noting that the half day or day that we spend with the whale sharks is a snorkelling opportunity rather than scuba diving. There is no minimum experience level required for this trip, but all divers need to have buoyancy control and other skills required for open water certification. We will have dive guides in the water on all dives to assist our guests
SWIMMERS
A trip like this is heaven for swimmers. Beautiful warm water, lots to see, and lots of adventure. You’ll be traversing deep into the Sea of Cortez, exploring little-visited areas that very few people get to see. There has never been a swimming safari offered like this in Baja. To participate in a swimming safari based on one of our Liveaboards, you do need to be a competent swimmer. But don’t worry about fitness. You can swim as much or as little as you like, and you’ll get stronger every day. Support skiffs will be nearby. Whether you swim very little or, for hardcore summers, you might swim up to 10 km a day, the choice is yours.
PADDLERS AND PADDLEBOARDERS
Self-reliant paddlers and paddleborders are welcome to head off on their own, subject to safety restrictions. Please let us know your experience and kayak preference well before departure. We have both single and two-person kayaks available. We have very high-end Seaward ocean touring kayaks that are very fast, but a little bit tipsy, and to delegate to be hauled up on rock beaches or alternatively, we have some high-quality plastic touring kayaks that are a bit more stable and much tougher. We can arrange a guide for a minimum group size of six or a custom guide can be requested by prior arrangement.
FOR THOSE INTERESTED IN THE ADVENTURE
Come and join us! There will be opportunities to go ashore, hike in the desert, and we will do our best to arrange a tour to view cave paintings. You’ll also have the chance to snorkel with whale sharks, and most likely go ashore on remote Isla San Pedro martir*, home to one of the largest populations of bluefooted and brown boogie birds in the world. Additionally, you can snorkel with sea lions, jump in the water with a pod of dolphins, try your hand at kayaking or paddleboarding in North America, climb the Ridgeline on Isla San Francisco, enjoy beach walks, hike through the desert, and much more. \n * We are fully permitted to go ashore at Isla San Pedro martir which is a special and unique privilege. Please note that a storm in 2023 wiped out part of the path making it much more difficult to traverse the island. Large numbers of sea lions on the beach can also make landing difficult.
SAFETY
Safety, excellence in guest experience, and the happiness of our guests are the cornerstones of our operations. Nothing is more important than your safety. At Nautilus and Baja Expeditions, we are proud to be the only operation in the world with ISM certification and external annual audit of our safety management system. This is the same certification that the largest cruise ships on the oceans hold. We strictly adhere to written processes, procedures, and protocols, and our captain and crew are trained into both initially, and with annual recurrent training. Every activity starts with a briefing on a whiteboard on board. All drivers must be equipped with an SMB and dive alert, which we provide as needed. Any guest participating in water activities must be equipped with a Nautilus Lifeline, emergency radio, and GPS device. We carry AEDs and extensive medical kits with a contract medical officer available to receive our sophisticated satellite communication system.
What do I need to pack?
Personal toiletries. Dive gear (or travel light and use our rental gear). Summer wear, noting that nights will be cooler. It can be very hot in the desert this time of year. Sunscreen (reef-safe sunscreen will be available on board with our compliments), towels, bed linen, soap, and shampoo are provided on board.
Do I need a passport?
Yes, and it must be valid six months from entry date
Do I need to obtain a visa ahead of time?
Only for a very limited number of countries. Please check the requirements for your country.
Do I need insurance?
Guests are required to have medical and evacuation insurance from a recognized provider before participating in any of our activities. Click here. to purchase coverage. We highly recommend this provider because they are very dependable, reliable, and their policies are reasonably priced. Other providers may not offer the same level of reliability. We also highly recommend the optional purchase of trip interruption insurance, which covers everything from cancelled flights, weather-related delays, lost baggage, and reimbursement if another guest has a medical issue that affects your trip. If you decline coverage, please know that we do not issue credit refunds for anything that’s beyond our immediate control.
What airport do I fly into?
SJD Los Cabos international has very convenient and nonstop connections to many different cities. Flying into LAP la Paz is also possible.
When should I fly in?
These trips are planned around the guests having the option of flying in and going straight to SeeCreatures to check in and then board the ship later that day. We recommend flying in several days early to take full advantage of our hospitality and all the neat stuff that we offer as pre-trip extensions.
How do I get from SJD into town?
Sealine Cabo transfers is our recommended provider of airport transfers to and from SJD. For booking please email Martin at: mmoreno@sealinecabotransfers.com We also recommend Miguel from Fara Nuevo as an alternative option. Email: mfc949@gmail.com Phone: +52 (624) 141 6254
How do I get from LAP into town?
We can arrange to pick you up. Please directly contact with our Concierges: concierge@nautilusdive.com
Can you recommend a local hotel?
Yes. For sure. We have our favourite hotels that we recommend and we have arranged discounted rates for Nautilus and Baja Expeditions’s guests. For hotel recommendations, or any other pre-trips, questions, concerns, or comments, please contact our concierge’s directly: Phone: +1 (604) 241-1918 – Please ask for Daniela or Maria WhatsApp: +1 (604) 360-9400 Email: concierge@nautilus.com
What is NOT included in the trip price?
Bar, gift shop, high-speed Internet connection, rentals, nitrox, crew gratuities. A $35 port fee must be paid on board in cash at the end of the trip.
Do you have a storm policy?
We highly recommend trip interruption insurance, which will cover you in this unlikely eventuality.
Where do we meet our boat?
When you arrive in town, please drop by SeeCreatures Cabo San Lucas location at Calle Miguel Hidalgo 10, Centro CSL. C.P. 23450, Cabo San Lucas, BCS. We will help get your kit up with whatever you need and hopefully get you out on pre-trip diver activities. Our SeeCreatures locations are normally open from 8 AM to 5 PM, but will stay open later on boarding days. We encourage you to check in early on boarding day, and drop off your luggage so that you can wander off and enjoy town.
Are you joining us in Cabo?
Please be at SeeCreatrues Cabo and for your transfer to La Paz, 4:30 pm latest.
Are you joining us in La Paz directly?
Please contact our concierge’s to confirm the meeting place and time
Can you help me get dive certified before the trip?
Yes. We specialize in introducing as many people to scuba diving as possible. We offer a full array of diving courses at SeeCreatures.
Can I get nitrox certified before we leave on the ship?
Yes, we could do it. This is a one day course at SeeCreatures.
Will I need to show proof of insurance, and if I'm a diver, adive certification card before boarding?
Yes.
Will I get seasick on this trip?
This time of year, the Sea of Cortez is generally quite calm. If anyone is worried about seasickness, we recommend the prophylactic use of the scopolamine patch. This is the perfect trip and destination for anyone looking for a smooth as possible experience at Sea. Please note that all of our steel ships are stabilized.
How much experience do I need if I'm a diver?
Your experience doesn’t matter. If you’re not certified, we can arrange a discover scuba experience. If you’re an experienced and self-reliant diver, you’re welcome to head off on days by yourself, and do your own thing if you wish, with the sole exception of diving in a national park where diving must be done with a guide. Our dive guides are always available for whoever wants to dive with us.
Are the boats camera friendly?
Of course! We have lots of housed GoPros available for rent and we offer a complimentary photo workshop at 1 pm. before every departure for those meeting us in Cabo.
What time do we arrive back in port?
Reminder that most Sea of Cortez trips board and return to La Paz with an included transfer to SeeCreatures Cabo San Lucas, or SJD Airport. We are usually back in port by 8 am. Disembarking by 8:30 am after breakfast. It’s a 2-1/2 hour transfer to SJD. For that reason we recommend booking your outward flight 2:00 pm or later.
Can you accommodate special dietary requests?
Yes, with reasonable advance notice, we are pleased to accommodate vegetarian, vegan, lactose, intolerant, gluten, free, low sugar, quasi-kosher and quasi-halal. We are likely unable to accommodate other special dietary requests, or guests with severe allergic challenges.
