Hidden Gems in the Sea of Cortez: Our Top 5 Cruising Spots in Baja
- Abbey Seeley
- May 13
- 6 min read
It’s one thing to read about the Sea of Cortez or hear whispers of its magic from fellow cruisers, but it's another thing entirely to experience it for yourself.
Over the past two months aboard Atlantean, we’ve explored stretches of this remarkable coastline that felt untouched by time, each anchorage offering its unique blend of rugged beauty, marine life, and that peaceful solitude only the sea can offer. In this post, we’re sharing a few of our favorite hidden spots- places that don’t always make the charts but deserve a spot on every cruiser's radar.
The Sea of Cortez
There’s something almost mythical about the Sea of Cortez- a place where desert mountains tumble into turquoise waters, and sunsets are referred to as "burning baja" due to their uniquely intense colors. Often called “the world’s aquarium,” this stretch of sea is teeming with dolphins, whales, rays, and turtles, making every day on the water feel like a nature documentary come to life. It was high on Adam’s list of must-sail destinations from the start, while I’ll admit I was eager to move on to the South Pacific islands, but it didn't take long for me to be absolutely blown away. The landscapes, which Adam refers to as layers of the Baja, due to the incredible mountain ranges that seem as if they go on forever, the wildlife, and the stillness are beyond what I could have imagined. It’s wild, raw, and endlessly beautiful.
While my previous posts detailed each and every stop consecutively and the events that took place, I quickly realized that maintaining that format would be a challenge, considering we visited 30+ anchorages in the Sea of Cortez. Since no one has time for that, we narrowed it down to our top five places.
Punta Pulpito
GPS: 26°30.861' N, 111°26.987'W
Why it’s special: Along a stretch of low-lying land, a magnificent, dramatic cliff rises sharply from the sea, creating stunning sunset views and shelter from northerlies.
Activities: Snorkeling around the rocky point is excellent, and a short hike up the ridge rewards you with breathtaking coastal views.
Tips: If you go ashore, plan on anchoring as the beach is very rocky. We managed it with one anchor but saw another group that used two, which seemed to work well for them. When we left, our anchor was stuck between rocks and took some finesse to retrieve in chest-high water.
Santa Rosalia
GPS: 27°20.264'N, 112°15.788'W
Why it’s special: A darling and quirky copper-mining town with a unique French influence- think iron church designed by Gustave Eiffel. Great for provisioning and a taste of Baja history.
Activities: We explored the historic center, visited the mining museum, and hiked to the cemetery on the hill. The plaza across from the Malecon had the best tacos we had in the entire Sea of Cortez!
Tips: The marina offers reliable services. It is a good stopover for reprovisioning and topping up fuel or water. Laundry services are available; you need a WhatsApp number, and a sweet lady will pick up your clothes at 9 a.m. and drop them off at 6 p.m. Drop off and pick up all done at the parking lot at the top of the ramp. Super convenient!
Our Experience: We stopped at Santa Rosalia twice, once on our way north and again on our return south. Both times, we got a slip at the marina since the price was so affordable. While there, we took advantage of the dock space and busted out our sewing machine for the first time to make dodger window covers and a shade cover for the cockpit.
Highlights: We met our new friends Phil and Steve during our first stop, and both encounters left a lasting impression. One afternoon, Steve motored up in his dinghy. He said something along the lines of “Your Fast Passage looks a lot like my Fast Passage!”- and sure enough, he's a proud new owner of Fast Passage 39. Considering only about 40 of these boats were ever built, the odds of crossing paths were slim, making the moment all the more special. We swapped boat tours—us aboard his Cats Paw Four, and him aboard Atlantean—and bonded instantly over shared design quirks and sailing stories. Meanwhile, Phil, a solo sailor with a beautifully outfitted catamaran, quickly became someone we genuinely clicked with. We spent hours in easy conversation, trading ideas and laughter. Our time with him was one of those unexpected gifts cruising can bring: strangers who feel like old friends almost instantly.
On our second stop in Santa Rosalia, we woke up one morning to an unexpected sight- The Western Flyer was docked in the bay. It was wild to see the very boat that had inspired so much of Adam’s fascination with the Sea of Cortez, such a pleasant surprise! Ironically, Adam had just started rereading it when we spotted the restored vessel.
Photos courtesy of Phil, who saw the Western Flyer at Playa de Agua Verde, B.C.S., Mexico
Pictures from Santa Rosalia, B.C.S., Mexico
San Francisquito
GPS: ~28.47°N, 112.86°W
Why it’s special: A serene double cove with excellent protection from most directions, San Francisquito feels like a remote haven halfway between Santa Rosalía and Bahía de Los Ángeles. The water here is a vibrant blue, often glassy calm, and the surrounding hills glow red at sunset.
Activities: We spent our days here in awe of the towering cactuses that dotted the landscape, ventured out for some light hikes, and, best of all, enjoyed some incredible spearfishing. While hiking, we found a little notebook hidden under a rock that invites you to sign it. We didn't have a pen, so we left one of our business cards instead.
Tips: Anchor in the inner cove for better shelter from swell. There’s no provisioning here, so come well-stocked. Sometimes local fishermen stop by for a chat or to offer fresh catch.
Highlight: The spearfishing turned out to be the highlight of our stay here and is the reason this place made the top five list. The underwater landscape just off the point was breathtaking, with rocky ledges and an abundance of marine life.
Isla Salsipuedes
GPS: ~29.93°N, 114.27°W
Why it’s special: Isolated, rugged, and wild- this island lives up to its name (“Leave if you can”). It's often overlooked, making it perfect for solitude seekers.
One of the most mesmerizing sights was the seabirds, which seemed to follow a continuous flight path around the island, effortlessly riding the thermals created by the steep cliffs. They circled in a rhythmic loop, using the updrafts like invisible highways.
Activities: Incredible underwater terrain for spearfishing with large pelagics sometimes spotted nearby. Hiking on the small island is easy yet enjoyable.
Tips: Anchor only in settled weather—exposed and rolly if conditions change. Bring everything you need; there's nothing here but nature.
Downside: If you're like me and have the kind of blood that attracts bugs, be ready for them. Adam had a few bites, but I was completely covered, and these weren't typical mosquito bites. They were so itchy that it felt like my skin was burning. It was awful, and truly the only downside of the Sea of Cortez. It seemed that the farther north we went, the worse the bugs got.
Video of drone footage from Salsipuedes Island
Photos from Isla Salsipuedes
Isla Mejía – Puerto Refugio (Isla Ángel de la Guarda)
GPS: ~29.52°N, 113.54°W
Why it’s special: I saved the best for last. This is one of the most remote and dramatic anchorages in the northern Sea of Cortez, where towering cliffs, hidden caves, and surreal silence create a setting that feels completely untouched.
Activities: Dinghy adventures along the cliffs and into sea caves, beachcombing, birdwatching, and the clearest water we've ever seen.
Tips: Several coves offer protection depending on the wind direction. Keep an eye out for strong katabatic gusts at night, and be sure your anchor is well set.
Downside: BITING BUGS.
Our Experience: We had an unforgettable time spearfishing at Isla Mejía. The underwater landscape was nothing short of mesmerizing: rugged, rocky terrain, crystal-clear visibility, and marine life in every direction. We swam alongside sea turtles, reef sharks cruising the depths, and watched schools of fish shimmer in the light. It was the kind of diving that makes you lose track of time, fully immersed in the rhythm and stillness below the surface. Just a short distance away, on a nearby island, we came across a massive colony of sea lions sprawled across the beach- more than I’ve ever seen in one place- barking, lounging, and soaking up the sun like they ruled the shoreline.
Video from Isla Mejia- Puerto Refugio
Reflections from the Sea of Cortez
The Sea of Cortez surprised me in all the best ways. What I once saw as a remote, dusty stretch we’d pass through on our way to the South Pacific has become a highlight of our journey, full of unexpected friendships, quiet anchorages, and jaw-dropping landscapes that feel like they belong on another planet.
From the steep cliffs of Punta Pulpito to the distant sound of sea lions at Puerto Refugio, these five anchorages have captured a part of our hearts. For anyone sailing this region, know that it’s more than a stopover- it’s a destination worth savoring.
Wow, it just gets better and better, The Photos are wonderful and the way you describe everything brings it to life. Thanks again,can’t wait for the next one.
Great writing and pictures. Thank you for sharing.
Love this post. The pictures are fantastic. Did you take them with just your phone. You write with such depth and clear description. Love your journey!!