Yacht Destinations in Baja California Sur: Where to Sail, Anchor & Explore

Starting from the southern tip of the Baja Peninsula in Cabo San Lucas, you’ll find nearly an endless array of enticing destinations for a yacht charter in Baja California Sur—and that’s just the east coast along the Sea of Cortez. Between Cabo and Santa Rosalia, the furthest town north before becoming the state of Baja California, there are over 437 miles of spectacular coastline and numerous islands, idyllic beaches, and stunning turquoise waters. 

As a resident of La Paz, I’ve been lucky enough to explore much of the peninsula by water—it’s one of my favorite things to do, especially in the wintertime when a wide range of whale species are often spotted. As there are so many enticing destinations along the Pacific Coast, we’ll focus on the best yacht destinations in Baja California Sur on the other side of the peninsula. The Sea of Cortez is typically much calmer and clearer, provided you avoid the tropical storm/hurricane season between July and October. 

Cabo San Lucas

Catering to everyone from the average traveler to all sorts of VIPs, from Hollywood stars to CEOs, Cabo San Lucas needs no introduction. It boasts a glamorous collection of designer shops, luxurious resorts, beach clubs, iconic bars, and fine dining restaurants serving Kobe beef, lobster, and Beluga caviar.

The scenery, including Cabo’s iconic rock formations like The Arch, rising from the water where the Sea of Cortez meets the Pacific, will leave you breathless. You’ll find plenty of dazzling beaches with fine golden sands edging a vibrant underwater world for snorkeling or diving among colorful fish, along with a wealth of other watersports, from kayaking and jet-skiing to parasailing and powered hang-gliding. It’s also a sportsfishing capital, with the chance to catch marlin, sailfish, tuna, wahoo, mahi-mahi, snapper, grouper, and more. 

The primary spot to anchor is the Cabo San Lucas Marina, providing a secure harbor for vessels of all sizes, including mega-yachts. There are also places for informal anchoring closer to resorts and beaches like popular Medano, but the marina is the most convenient and provides better shelter.

Isla San Francisco

Located about 50 miles north of La Paz, Isla San Francisco offers one of the most stunning anchorages in all of Mexico. It has a vast crescent bay with bright white sand and vivid turquoise waters backed by fiery red hills, creating a colorful scene. Enjoy relaxing on the dramatic sweep of the beach, or take a hike on one of the multiple trails traversing the desert landscape with giant cacti, and along the rocky ridgeline on the south shore. It’s the perfect vantage point for a stellar view of the island and the brilliant blue of Amortajada Bay, as well as to capture photos. This is also a haven for birdwatchers with the chance to spot blue-footed boobies and many other types of seabirds.

Los Barriles & Cabo Pulmo 

Los Barriles is located on the East Cape of the peninsula on the Sea of Cortez. It offers sandy bottom anchorage and is ideal for exploring the town and nearby Cabo Pulmo, a protected marine park. The park boasts vibrant reefs and abundant marine life, but anchorage is limited. Los Barriles is more accessible with numerous facilities and a bay that’s protected from the open sea. There are many beautiful beaches throughout the area for sunbathing, swimming, or even horseback riding on the sand. Taking an ATV tour (or renting one) is popular for desert exploration, and there are even waterfalls to explore in the mountains nearby. 

In the town of Los Barriles itself, there’s a lively Saturday community market, fun shops, and numerous eateries for savoring authentic local cuisine, including lots of fresh seafood.

Isla Carmen

While many people enjoy boat tours to Isla Carmen from Loreto (about a 90-minute journey), you can head there on your own. Cruise the coast, watching for bighorn sheep that can be seen clamoring the rocky hillsides and a wealth of birdlife, including osprey and blue-footed boobies. Afterward, take advantage of the excellent anchorage in V-Cove on the northern side of the island. 

Isla Carmen is home to many postcard-perfect beaches to relax on and swim or snorkel from, plus you can even explore an ancient salt mine that was once the largest in the world. There are many relics from the past, including old buildings that played an important role in the saltworks operation, such as abandoned homes, a church, and a school, with many still retaining the original furniture. 

Isla Coronado

While it’s just a short distance north of Isla Carmen and Loreto, Isla Coronado is well worth a visit of its own. About midway up the west coast of the island, you’ll see a rocky islet called Isla Mitlan. It forms an open wedge for anchoring between Coronado and Mitlan. The channel walls are particularly ideal for snorkeling in the clear turquoise water that’s been called the “world’s aquarium” by the renowned late oceanographer Jacques Cousteau. 

Isla Coronado also boasts an unspoiled white sand beach and opportunities for birdwatching, including blue-footed boobies, and hiking. On the back side of the island is a colony of sea lions. There are no shops or restaurants, but there are also aren’t any tourist crowds, providing an incredibly peaceful setting.

La Paz

La Paz is the vibrant capital of Baja California Sur, with multiple marinas to choose from, including Marina CostaBaja, where you’ll have access to a wide range of watersports and picturesque beaches. You’ll be near the 3.1-mile-long Malecon (waterfront promenade), ideal for strolling and cycling, complete with a dedicated bike lane. Along one side are beautiful sea views, and on the other, a variety of shops, bars, and restaurants. You’ll also find benches to rest on while watching the world go by, and some outstanding public art installations that make for great photo ops with the turquoise Sea of Cortez in the backdrop. 

One of the top things to do is to visit nearby Balandra Beach. Often ranked among the most beautiful in all of Mexico, it’s known for its unique “mushroom” rock that was sculpted by the winds and the waves, as well as its clear, shallow turquoise water. The number of visitors is limited due to its popularity, but you can anchor here without worry to explore, swim, and snorkel among schools of colorful fish.

Punta Chivato

Closer to the stateline of Baja California, just north of Mulege, Punta Chivato offers easy anchorage with a gently sloping sandy bottom while providing an ideal vantage point for sunrises. This relatively secluded area offers breathtaking natural beauty, from the rocky cliffs to sandy beaches with clear, cobalt waters. There’s only a small population of residents, with the night sky so dark that stargazing is one of the main attractions. By day, the beachcombing is fantastic, with shells scattered in various colors, shapes, and sizes as far as the eye can see along its shores. It’s also considered one of the best spots for fishing, particularly for yellowtail. 

Espiritu Santo Biosphere Reserve: Los Islotes, Espiritu Santo & La Partida

Part of the UNESCO-listed Espiritu Santo Biosphere Reserve, a protected archipelago of volcanic islands near La Paz, Los Isolotes, Espiritu Santo, and La Partida are renowned for their diverse underwater ecosystems and abundant marine life, from tropical fish, eagle rays, and sea turtles to dolphins and sea lions. They also boast dramatic landscapes with unique rock formations and pristine, white sandy beaches, beautifully contrasted by the cobalt blue sea. 

Los Isolotes is the island known for its sea lion colony, where visitors can even snorkel among the curious sea lions and their pups. They’re often quite playful, sometimes tugging on your life vest straps. On Espiritu Santo, walk along a canyon arroyo to enjoy a view across the islands. La Partida offers unspoiled white sandy beaches that are only accessible by boat, resulting in total tranquility and the opportunity for an unforgettable swim. Keep in mind that there is no overnight anchoring at Los Islotes; in fact, you might want to return to nearby La Paz for the night.

Puerto Escondido

Just 15 miles south of Loreto, Marina Puerto Escondido offers an upscale vibe and a tranquil spot for anchorage. A naturally protected, “hidden” harbor, it makes a great base for hiking or mountain biking in the rugged Sierra de la Giganta. Just across the highway, you can trek through picturesque Tabor Canyon, which is often referred to as Steinbeck Canyon thanks to Nobel Prize-winning writer John Steinbeck, who described it as an oasis in The Log from the Sea of Cortez. The marina complex itself offers outstanding modern facilities, including a restaurant selling wood-fired pizza and a grocery store. 

Loreto

Loreto is a popular place to begin a yacht charter as the gateway to Loreto Bay National Park, and it’s a must-visit when traveling north from Cabo San Lucas or La Paz. The park itself is often referred to as the region’s own “Galapagos,” with 800 different animal species that can be spotted here. In the winter, watch for blue whales, fin whales, and humpbacks. If you dive or snorkel in this underwater paradise, you might find yourself alongside sea turtles, manta rays, or even sea lions.

If you’re interested in the opportunity for very close encounters with Baja’s famous “Friendlies,” the gray whales who come to the lagoons along the Pacific coast to give birth to their calves, join a tour departing from Loreto. Many of these whales are quite curious and seem to enjoy interacting with humans, bringing their babies right up to the boats as if to show them off.

In the charming town of Loreto itself, you’ll find plenty to do. It boasts a rich cultural heritage with multiple museums, historical landmarks, and outstanding eateries. Be sure to set your alarm early to catch a sunrise from here – the colors that fill the sky are one of the most impressive works of Mother Nature you’ll likely see. 

Santa Rosalia

Santa Rosalia is the last stop in relative civilization before sailing into the northern Sea of Cortez and the state of Baja California. Marina Santa Rosalia is the older, more basic marina, while Singlar Marina on the left side of the harbor, closer to town, provides a modern facility with many amenities like floating docks, fuel, Wi-Fi, power, water, a pool, and a bar. 

The town is picturesque with a rich history and unique charms. It was founded as a mining town in the late 19th century and has managed to retain much of its character from the past. Some have described it as reminiscent of Catalina Island in California, but you’ll notice significant French influence in the architecture. While there are plenty of restaurants, the French bakery is most notable. El Boleo is one of the most famous bakeries in all of Baja. More than a century old, it still uses some of its original imported machinery.