The call goes out over the ship’s PA system: “Dolphins at 12 o’clock”. It’s dawn on the Sea of Cortez, a narrow strip of water wedged between the Baja California Peninsula and the Mexican mainland, and this is a wake-up call that simply cannot be ignored.

Passengers quickly gather at the bow of the National Geographic Sea Bird, a ferry turned expedition vessel. Ahead, white caps punctuate a horizon slipping from the inky darkness of night, the first rays catching distant movement: the vanguard of an approaching pod, the dolphins effortlessly leaping through the water as they race towards the ship.

“Bottlenose dolphins,” proclaims expedition leader Larry Prussin from his perch outside the wheelhouse. “There looks to be about 150 of them. What a way to start the day!”

His excitement, even after his many years of exploring the world’s oceans, is infectious and it’s quickly standing room only at the bow.

After an hour of riding the Sea Bird’s wave, the dolphins turn east as one, as if choreographed, only to be replaced by a pair of blue whales, their fine spout spray lingering in the still morning air. The tiny dorsal fins that slice through the water belie the gentle magnitude of the world’s largest animal below.

It’s the first day of our week-long Lindblad Expeditions-National Geographic adventure cruise through a body of water that has enchanted navigators, explorers and naturalists for centuries. Also known as the Gulf of California, the Sea of Cortez is an aquatic wonderland without equal; fed by great rivers such as the Colorado, the Sinaloa, the Sonora and the Yaqui, the gulf, dubbed “the world’s aquarium” by explorer Jacques Cousteau, is one of the most diverse seas on the planet, home to more than 900 fish species, fevers of graceful manta and devil rays and colonies of grinning sea lions, as well as dolphins, of course.

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Full of life it may be, but the Sea of Cortez is also a fragile ecosystem on the brink. Fishing sustains many of the communities that surround it and overfishing and poach­ing have taken to the edge of existence some of its species, including the endemic totoaba fish, prized in traditional Chinese medicine, and the vaquita, the world’s most critically endangered marine mammal, the numbers of which have been decimated by illegal gill nets. With fewer than 60 of these shy porpoises remaining, it was recently announced that dolphins trained by the United States Navy would help locate the last vaquitas before it’s too late.

That’s where companies such as Lindblad Expeditions-National Geographic come in. A collaboration between one of the world’s oldest expeditionary companies and the natural sciences magazine, the eco-tourism cruise line has been plying the waters of the Sea of Cortez since 1977, its resident naturalists, biologists and adventurers guiding the intrepid and inquisitive along Baja’s moonscape coastline and into the desert interior of its many islands, home to towering cactuses, pristine coves and remote sea bird colonies. The hope is that awareness will foster a desire to protect.

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“There is nothing in the desert and no man needs nothing,” says naturalist David Stephens, quoting Laurence of Arabia, as he leads us on our first hike, on tiny, seemingly barren Isla Santa Catalina. “Clearly he never came to Baja!”

Within minutes we’ve learned about the island’s native rattlesnakes, its towering cactuses and the ladder-backed woodpeckers that make their nests within the spiky plants. As we trace a dry river bed inland, Nat Geo-certified photo instructor Linda Burback teaches alternative composition and expo­sure techniques to budding shooters, and when we reach the beach again, a flotilla of paddle boards and dayglow-orange kayaks stand ready for those looking to explore the island’s rugged coastline.

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On Isla San Esteban, we walk up a dry desert arroyo in search of nesting yellow-footed gulls and the island’s resident reptiles, the pinto chuckwalla and the spiny-tailed iguana, which like to laze atop cactuses. We watch hundreds of thousands of Heermann’s gulls and Elegant terns during a circum­navigation of tiny Isla Rasa, home to 95 per cent of the world’s population of both species, before visiting time-weathered Santa Rosalia, a former French mining town centred on an iron church designed by Gustave Eiffel.

In the protected biosphere of Isla San Pedro Mártir, squadrons of brown pelicans and double crested cormorants skim across the mirror-like seas and blue- and brown-footed boobies dance in the thermals. The roar of frolicking California sea lions echoes off towering cliffs from which indigenous Indians once collected guano. At Los Islotes, an important sea lion rookery, we snorkel with these inquisitive, puppy-like animals, which mesmerise with their aquatic dexterity.

On a zodiac cruise off Isla San Marcos, with its hidden coves scoured into the rock by the elements, we trail a grey whale and her calf; the youngster is the size of an SUV and breeches at its mother’s side, to the gasp of visitors and the whir of cameras.

“It’s all about awareness,” says naturalist Berit Solstad, as we quietly stalk the whales. “The more people who know about how special the Sea of Cortez is, the more they will want to protect it for future generations.” She points to the calf breeching once again. “Awareness is the only real hope that we, and this little fella, have left.”