The Magic of Magdalena Bay

There are many reasons Magdalena Bay became one of my favorite places in Baja California Sur. On my first visit with my friends, and on each trip with Dive Ninja Expeditions, I find a magical desert wonderland, that only becomes richer and more mind-blowing every time I return. Here are a few reasons why we love this place so much.


Magdalena Bay, or Bahía Magdalena in Spanish, is a 50 km long bay, and about 200 km of lagoons and channels on the Pacific side of the Baja California Sur, in the municipality of Comondú. It is protected by two islands – Isla Magdalena to the north and, Isla Santa Margarita to the south. Between these islands and smaller sand banks which separate the shallow bay from the Pacific Ocean, small channels let the water come in and out of the bay, bringing in fresh nutrients and clean water. This makes Magdalena Bay a very healthy and productive marine environment, hosting many species throughout the year. The south part of the bay is wide, with the more mountainous part of the islands as barriers. On the contrary, to the north the bay narrows to shallow channels, with thick mangroves growing on the sandy shores to both sides. These are the largest mangrove systems in the whole of Baja California peninsula. The contrast between the sandy desert dunes, the lush mangroves and the vast blue ocean are very distinct here, and create a mesmerizing view of colors and textures. It is indeed a special place, and people have recognized this fact many years ago.

Mangroves & dunes in Bahia Magdalena, Baja, Mexico
Map of Anian straight, 1600's


In 1539, Spanish conqueror Hernán Cortés, sent the explorer Francisco De Ulloa out of Acapulco to explore the Pacific coast of Mexico. In his travels, De Ulloa discovered that Baja California was actually a peninsula, not an island (though, this idea was still common until the 18th century, like this map from 1687). He named the gulf he has discovered the Sea of Cortez. He also found the beautiful Magdalena Bay on that journey. Later, in 1837, American whaling ships visited the area, harvesting oil and hunting Sperm whales on the Pacific side of the islands. In 1868 the United States had leased and established a ‘Coaling Station’ in the bay. Throughout the 18 hundreds, Magdalena Bay became a busy whaling area, with the discovery of the aggregation of California grey whales. American whaling ships were the first to hunt in the area, but once the word spread of Charles Scammon’s large numbers of landings of Grey whales, other countries started whaling here as well. In the whaling peak years of 1855-1866, an estimated 1250 whales were landed in Magdalena Bay alone. By the end of the 19th century, the Grey whale population in the area was almost extinct.

In the early 19 hundreds, when the world was turbulent and war was on the doorstep, a few countries attempted to lease the area, once the American lease was over in 1907. In 1908 the American ‘Great White Fleet’ of 16 battleships cruised around the world and stopped for some artillery practices in Magdalena Bay. And in 1912, just before the first world war, there were rumors that Japan tried to buy the harbor from Mexico. Moreover, both the German Kaiser and the Emperor of Japan are mentioned to have tried to utilize the bay in historian Barbara Tuchman’s 1966 book The Zimmerman Telegram. Some reports say Japanese submarines used the bay for shelter before the second world war, and an American submarine that disappeared in 1920 had been found just out of the bay in 2019. The International Whaling Commission banned Grey whale hunting in 1949, and the California grey whale population has been returning to Magdalena Bay every year since then, becoming the main tourist attraction in the area.

USS H1 submarine wreck, Bahia Magdalena, Baja, Mexico
Captain Melecio, Dive Ninja Expeditions Striped Marlin Expeditions, Magdalena Bay, Baja California Sur, Mexico

People and Industry

My second favorite thing about Magdalena Bay are the local people we work with. At Dive Ninja Expeditions we always try to support the people who live and protect the areas we run tours in. And they do an amazing job! There are only a few small settlements in the bay and along the large lagoon shores. The largest is Puerto San Carlos, a tiny fishing town located at the northern part of the bay, just below the elongated lagoons and extensive mangroves. The main industry here is artisanal fishing, sport fishing and eco-tourism. The artisanal fisheries produce shrimp, lobster, clams, and octopus in a sustainable industry and is limited to the inner parts of the bay. The waters out of the bay are a superb environment for larger, more exciting species. Sport fisherman come here to battle tuna, marlin, Mahi-mahi and other pelagic fish. There is even a tuna fishing tournament which attracts many visitors and competitors. But, there is also a big shark fishing industry on the outer side of the islands, which is not sustainable or very profitable. The eco-tours are what we are most interested in, and the options are various and plentiful. The islands, the mangroves, the bay and the open ocean all hold some amazing natural sights. I’ll talk about that in a moment (if you don’t mind…). Dive Ninja Expeditions collaborates with a few of the local operations in San Carlos, supporting the eco-tours and showing the community that there are sustainable ways to make a good profit, rather then exploiting endangered species.

Another special place in Magdalena Bay is Puerto Adolfo López Mateos. This little village sits in the north part, where Magdalena Island’s sand dunes are closer to the peninsula and create narrow waterways between the mangroves and the dunes. Fishing and eco-tourism are the main industries here as well, though the fishing part is not mostly artisanal such as in San Carlos. The village has a large cannery which processes mainly sardines and tuna, caught by industrial fishing vessels in the Pacific Ocean. Lopez Mateos is also considered one of the best places in the world to encounter Grey Whales. The legend tells, that during the whaling period, fisherman called the Grey whales Devilfish, as the whales would put up a fight when attacked by whalers, and many men were killed trying to land cows, bulls and calves. But one day, a small fishermen’s boat was approached by a lone Grey whale, and while the fishermen were terrified they were going to die, one of them put his hand out to the water. The whale in turn lifted it’s massive head to the hand and touched it, which was interpreted as a peace agreement between the fishermen and the gigantic ‘devil’.
Magdalena Island also supports a tiny village called Puerto Magdalena, which offers whale watching tours in season, as well as hiking & ‘glamping’ on the island. Santa Margarita’s only settlement is called Puerto Cortes, and is a naval base, with no permanent residents.

Gentle Giants expeditions, Puerto Adolfo Lopez Mateos, Bahia Magdalena, Baja, Mexico
Coyote on dunes, Bahia Magdalena, Baja California Sur, Mexico

The Best Part of All – Nature and Conservation

Already on the way to the towns and villages of Magdalena Bay, you’ll start seeing incredible natural environment and conservation efforts. Along the road, tall wooden poles, with platforms on their tops, have been placed to provide the ospreys and other marine birds safe nesting sites. Caracara and turkey vultures are also a very common sight, sitting on top of centuries old cardon cacti. These giant cactus trees are also protected by law. In fact, the whole area, including the islands, bay, lagoons and mangroves are all protected by the Mexican government. The locals make sure everyone complies to the rules of the protected area, and it is completely apparent they care about their natural resources. Many species live in the area year round, and bird watching, hiking and ‘glamping’ on the islands are great ways to admire the land and beaches of Magdalena Bay. The mangroves are a great place to see different kinds of heron, ibis, egret and many other coastal birds. Magdalena Island is also a habitat for bald eagles, coyotes and some rare endemic plants, and has the only natural source of fresh water in the whole area. Santa Margarita Island holds the seasonal hatching of the brown pelican chicks in spring. There’s even a tiny sand bank, in the middle of the bay, called the Bird Island where hundreds of cormorants, ducks and pelicans rest, until a boat comes by to make them soar to the sky and fly all around you.

But, the real best part, is the marine wildlife, and Magdalena Bay sure does deliver when it comes to unforgettable, unbelievable, breathtaking encounters. The most famous are the grey whales, which come to shelter in the shallow lagoons during the winter. After an amazing journey from the Bearing Sea where they feed, along the west coast of North America, they arrive to their destination, Magdalena Bay and the other lagoons of Baja California Sur. Here they mate, give birth and rear their young. Since the ‘peace treaty’ with men, they seem to really like interacting with people, coming right to the whale watching boats, rubbing along the sides of the vessels and even allowing people to touch them and splash them with water. It is not uncommon to have a full grown mama whale, bring her calf to the surface beside the boat for a long look. It is an amazing feeling looking a whale calf in the eye, realizing it is just as amazed as you are. Dive Ninja Expeditions gives you an opportunity to experience the incredible grey whale encounters in Magdalena Bay – our Gentle Giants Expeditions which take you all around Baja California Sur, including Lopez Mateos, to see not only the grey whales, but also blue and humpback whales, as well as whale sharks! We can also arrange a shorter excursion, to spend a couple of grey whales filled days in Lopez Mateos or San Carlos.

Grey whale calf and mother, Magdalena Bay, Baja California Sur, Mexico
Striped Marlin, Magdalena Bay, Baja, Mexico

Our more action filled expedition in Magdalena Bay is based out of San Carlos and is one of the most thrilling experiences I have had in Baja. Dive Ninja Expeditions and Nakawe Project work together to bring you the Striped Marlin Expedition, on which you can witness the Mexican sardine run and swim in the open ocean, along with marlin, sea lions, dolphins and gigantic bait balls of sardines, mackerel and anchovies. Nowhere else have I seen so many pelagic species on one trip! The bait balls attract not only one of the fastest fish in the sea, the striped marlin, but also a variety of other species that cross the area. Humpback, fin and even rare sei whales, orcas, mako sharks, bottlenose dolphins and California sea lions, along with many marine bird species, like frigates, boobies, sheerwaters, and many others are only some of the animals you can encounter on these mind-blowing expeditions. There’s nothing like swimming among the top predators of the sea, in their natural habitat. Seeing them look at you as an equal and giving you a turn at their bait ball, just to be confused by you not jumping on the opportunity. A real lesson in collaboration and sharing.

Want to explore the spectacular Magdalena Bay? Join us on one of our expeditions in the area to meet the people, animals and beautiful diversity this awe-inspiring place has to offer!

Frrediving Mobula expedition Dive Nina WExpeditions in Baja California Sur


Nature and outdoors is what I love most. Animals, plants and terrain. Always seeking adventures, exploration and learning something new. Love being a Ninja Instructor and Expedition Guide and showing people the beauties of the world. 
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