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