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Log from the Sea of Cortez and Laguna San Ignacio

By Roger Harris

I am pleased to share the following log from an Oceanic Society expedition to Baja California, Mexico's San Ignacio Lagoon and Sea of Cortez in March 2017. For a complete list of all vertebrate species sighted during our expedition, click here.

A friendly gray whale approaches our panga in Laguna San Ignacio. © Jose Sanchez

March 4, 2017 | Loreto

Our Baja California adventure officially begins at 6:00 pm as we gather in the hotel lobby. Our Mexican host Maria Najera introduces herself, her husband Rafael, and her young son Rafael. I also introduced myself (Roger Harris), as the Oceanic Society naturalist on this expedition.

We then walk around the block to a most interesting whale museum (Grupo Ecologista Antares A.C.) with articulated whale skeletons from the local area and other natural history exhibits. Fernando Arecas, the director of the museum, shows slides of the principal cetaceans (whales, dolphins, and allies) found here in the productive Sea of Cortez, which include:

  • Gray, fin, blue, sei, humpback, and Bryde’s whales (from the suborder of Mysticeti whales with baleen and no teeth);
  • Sperm and pygmy sperm whales (from the suborder of toothed whales or Odontoceti, in their own family of Physeteridae);
  • Common, Risso’s, and bottlenose dolphins, orca, and pilot whale (from the family of dolphins or Delphinidae also in the suborder of toothed whales or Odontoceti).

Fernando’s introduction to the marine mammals off of Loreto is illustrated with his professional photographs, the highlights of studying whales here for 34 years.

Another two blocks into town and we’re at the town square with its historic church. A festival is going on with dancers and other entertainers. But by this time we are ready for dinner.

The quaint town of Loreto was the first Spanish colonial settlement in Baja, established 1697. © Roger Harris

March 5, 2017 | Loreto

We have an early breakfast at the hotel’s second floor dining room, directly overlooking the Sea of Cortez, where the early risers witness a spectacular rosy sunrise over the water.

At 7:30 am, we walk a block up the malecón (the seafront avenue) with our animated local guide, Necky. Even before we get into the dock, we see a couple of distant whale blows highlighted in the early morning sun. This is an auspicious start, because our original plans were to cruise in the boat for about an hour to the south to find the whales. Instead, the whales have come to us.

We board a 27-foot open “super panga” (motorized open skiff) driven by Nacho and take off into the bay. The viewing conditions couldn’t be more perfect: flat calm, pleasantly warm, and fair skies. To the east is the protective Isla Carmen and to the west is the Baja Peninsula, punctuated by the dramatically serrated peaks of the Sierra de la Giganta (the giant range).

We enjoy a good three hours of unhurried observations of three blue whales, the largest of the whales, the largest of the mammals, and indeed the largest animal of all times (including being heavier than any of the dinosaurs). We witness the blue whales’ impressive columnar blows, and even at one point had the dubious pleasure of experiencing whale breadth up close and personal. After a series of blows and shallow dives, the whale would then go for a deep dive, usually showing its immense fluke (tail). It would then remain submerged for 5-12 minutes before surfacing to repeat the sequence.

A blue whale blows in the calm waters off Loreto. © Roger Harris

Lunch is on the desert island of Coronado, where a couple of palapas (gazebos) provide shade. The white sandy beach is framed by jagged black boulders. A couple of Eared Grebes paddle around in the brilliantly azure shallows. Isla Coronado is volcanic, and an eroded volcanic cone still crowns the uninhabited island clothed in nearly pristine desert vegetation.

Back on the boat we cruise past the flat Little Coronado Island. The nearly endemic (found only in a particular location – in this case the Sea of Cortez) Yellow-legged Gulls are perched on top of cardon cacti. A Great Blue Heron shows itself. The herons nest on the island among the cacti.

A Great Blue Heron perched atop the cacti of Isla Coronado. © Roger Harris

Royal Terns, a Snowy Egret, Double-crested Cormorants, Brown Pelicans, and Heermann’s Gulls loaf on the rocks along the shoreline. These handsome gulls are also near endemics for the Sea of Cortez.

A large male California sea lion is briefly spotted swimming a ways off. In the course of the morning, we also see a few Brown Boobies and Magnificent Frigatebirds overhead.

The rest of the day is at our leisure to catch up on sleep and explore Loreto on our own. Highly recommended are the old church and a museum at the town square.

March 6, 2017 | Loreto

Sunrise over the Sea of Cortez at 06:46 is seen from the hotel’s breakfast balcony. Within an hour, we are back on Nacho’s super panga, and within 5 minutes we have spotted blows from two blue whales. We linger with the whales for a few minutes. Necky says that one was feeding. We could see it swimming on the surface on its side, showing its belly pleats and pectoral fin.

The massive fluke of a blue whale in the Sea of Cortez. © Roger Harris

Two bottlenose dolphins languidly swim by. A couple of Brown Boobies and then four Blue-footed Boobies glide overhead. Later an adult female Magnificent Frigatebird soars above us.

But we want to visit new waters, so the boat cruises full speed ahead for about a half hour in the marine Parque Nacional Bahia de Loreto past the craggy Isla Danzante on the west and the islands Montserrat and Santa Catalina further south and to the east. To call this setting scenic would be an understatement.

A handful of blue whales are spread out over the calm waters. Visibility is good. Sometimes we see the characteristic towering columnar blow of a blue whale so far away that there is a time delay between the visual perception and hearing it.

Toward the end of our stay, we get close looks of two blue whales milling about and again get to experience whale breath. The wing tips of a passing manta ray cut through the sea’s surface.

By late morning, the seas are changing to choppy as a fresh breeze descends upon us. Rather than fighting the waves for the 25-mile boat ride back, Necky calls on the boat’s radio for a van to come pick us up at the appropriately named Puerto Escondido, where we head ashore and disembark. By early afternoon we are back comfortably at our hotel with the rest of the day at our leisure.

March 7, 2017 | Loreto – San Ignacio – Laguna San Ignacio

After two days of perfect whale watching weather, the winds have definitely picked up this morning. Fortunately for us, today we’re traveling to the other side of the Baja California peninsula.

Packing into a van driven by Necky, we head up the coast on Highway 1. The Sea of Cortez is to the east, the Giganta Range to the west.

At the small palm oasis hamlet of Rosarito, we stop to see the characteristic vegetation of the Central Gulf Coast Desert. The columnar cardon cacti are a visual dominant among the red-flowered Palo Adan, a variety of chollas (jointed cacti), and some elephant trees.

Further up the coast, we pass through the village of Mulegé with its extensive palm oasis. At Santa Rosalia, a port town for a copper mine, we head west and inland.

We climb up into the Sierra San Francisquito (mountains). Here a somewhat drier, more sparsely vegetated desert has patches of tree yuccas and extensive stands of creosote bush. To the north is the dramatic, but dormant Volcán Tres Virgenes, one of the tallest peaks on the peninsula.

The mission in San Ignacio, founded 1728. © Roger Harris

We stop at the village of San Ignacio for lunch and a visit to the old church. The historic mission was founded in 1728. The town is on the palm-lined Rio San Ignacio River, one of only two major rivers amidst the desert on the peninsula.

As we proceed west, the paved road gives way to a sometimes wash-boarded dirt road as we enter the Vizcaíno Desert, which is a Biosphere Reserve and one of the largest preserved natural areas in all of Latin America.

Cardon cactus dominate the Vizcaino Desert landscape. © Roger Harris

The mountain slopes give way to a flat plain with brilliantly white salt pannes punctuating this new desert landscape with its low, sparse, shrubby vegetation.

The road leads to Laguna San Ignacio. We pass a number of seasonal whale watching camps and some local fishing encampments. Along the road in places are piles and piles of clam and scallop shells from the local fisheries. We see at least two large stick nests on platforms, attended by Ospreys.

By late afternoon, we reach our safari-style tent camp. Gray whales spout out on the adjacent lagoon. Camp naturalist Debbie, from Switzerland, greets us and takes us on a tour of the camp.

Soon it is happy hour and time for beers or margaritas as we watch the sun set over the lagoon. After a delicious tamale dinner, camp manager José gives us an introduction to camp life, before we retire to our tents in the moonlit night.

March 8, 2017 | Laguna San Ignacio

In the pink light of dawn, an Osprey deposits nest material on top of the camp’s water tank. The Osprey population of the lagoon is known for being ground nesting on this treeless plain. But every structure that approximates a tree, even the camp water tank, is a target as a nest platform.

Hot beverages and cold cereal are available for an early breakfast at 7:00 am, followed by a hot breakfast at 8:00 am. Then we are fitted with PFDs (personal floatation devices).

By 09:00 the jolly Oceanic Society group is in a panga with driver Martín “The Whale Kisser” and guide José. Within 5 minutes we are in the designated whale watching area, where we are limited to 1.5 hours at a time as a conservation measure.

We are simply surrounded by gray whales. Wherever we look, there are blows, some flukes, and even a few breaches. The scientists studying this population estimate that there are about 75 cow/calf pairs and as many as 120 single whales in the lagoon this time of year. The cow/calf pairs will linger a bit longer, but the single whales are quickly leaving for their northern feeding grounds.

A friendly gray whale approaches our panga. © Jose Sanchez

A small group of gray whales are roiling about is what is colloquially called “hanky panky” by whale watching guides. More precisely, a female is being courted so-to-speak by some males who are hopeful that she will be receptive. By this time in the gray whale’s migration cycle, however, most of the females without calves have already been impregnated and have left weeks ago for the northern feeding grounds.

A green turtle is ever so briefly glimpsed on the lagoon’s surface, before it dives out of sight. Historically, this area had a commercial turtle harvest. In modern times, both the turtles and the whales are strictly protected by the Mexican government.

A pair of bottlenose dolphins cruise past us.

Then a cow gray whale and her newly-born calf approach our panga. They turn out to be “friendly whales.” We were expecting such behavior—that’s the primary attraction in making a trip to this remote area—but our expectations are so exceeded by the reality of these wild creatures repeatedly coming up to our boat and presenting themselves to be touched. It was overwhelming.

Passengers enjoy an intimate encounter with a gray whale. © Jose Sanchez

Back in camp, some of us briefly paddle kayaks in the mangroves. Soon it is time for a delicious lunch al fresco of fish and scallop tacos.

The afternoon is a repeat of the morning’s—yes—awesome experience with friendly whales. What a thrill it is to get sprayed by a whale’s blow within an arm’s distance! Our guide for the afternoon is Debbie and the driver is Chavalo.

A curious gray whale calf. © Jose Sanchez

By now, we’re settling into the camp routine of happy hour watching the sun recede over the lagoon. José tells us how this vast El Vizcaíno Biosphere Reserve was created, working in cooperation with the local communities to develop responsible tourism.

Then we have dinner as the cool of evening approaches. Afterward, José tells us the entertaining story of first encounter with friendly whales in 1967 by a local fisherman and how it got publicized in 1972 in Reader’s DigestReader’s Digest.

A coyote out on the desert plain sings into the night.

March 9, 2017 | Laguna San Ignacio

An early morning fog envelopes camp, not an uncommon weather condition along this Pacific coast. The desert plants derive much of their moisture from fog drip in this very arid region.

We go out in a panga with guide José and driver Chavalo. On our cruise from camp to the designated whale watching area, Sheridan, with professional voice, entertains us with operatic song putting us all in an especially festive mood.

Just when we thought it could not possibly be better than yesterday’s close encounters with whales, today’s experience tops that. One cow/calf pair stays with us for almost a half hour. The calf even opens its mouth and allows us to touch its baleen plates.

A friendly gray whale calf shows its baleen plates. © Jose Sanchez

We also see both Parasitic and Pomarine jaegers, aggressive relatives of the gulls. These seabirds make a living during the non-breeding season primarily stealing fish from terns and other water birds. In the breeding season, jaegers nest in the far northern tundra and specialize in capturing lemmings.

This afternoon’s panga excursion is with guide Debbie and driver Martín. Any number of cow/calf pairs come close and investigate us, but none stay to be petted. We did, however, get to see some really interesting behaviors up close.

Sheridan, accompanying himself on ukulele, serenades the group during happy hour as we watch the sun set over the lagoon.

After dinner, José and Elizabeth’s 13-year-old son Esteban gives an accomplished slide talk on the history of commercial whaling, followed by naturalist Debbie’s presentation on gray whales. José then shows his remarkable GoPro photographs and videos that he took of us interacting with the friendly whales.

March 10, 2017 | Laguna San Ignacio

After a mildly windy night, the wind subsides for a beautiful sunny day. We join guide José and driver Martín in a panga and head across the lagoon, where we cruise through a maze of channels lined with red and white mangroves.

Next we head out to the whale watching area, getting close to the breakers at the mouth of the lagoon. We are joined by a friendly cow/calf pair. Not only the baby but the mother repeatedly come in close to be petted for yet another exhilarating experience.

© Jose Sanchez

Our afternoon panga ride into the whale watching area is enjoyable, but we are not joined by any friendly whales this time.

Happy hour is exceptionally so with margaritas and scrumptious barbecued black bass. The occasion is especially festive because it is Judy’s birthday, giving us occasion to toast her and sing Happy Birthday. After taking a group picture, we get to see the fabled “green flash” – really a glimmer – just as the sun goes down below the horizon.

After dinner, José gives an informative presentation on whale biology, complete with his accomplished imitations of whale vocalizations.

March 11, 2017 | Laguna San Ignacio – San Ignacio – Loreto

Our final whale watch this morning is with driver Martín. We have close encounters of the petting kind with two different cow/calf pairs. Even the cows are friendly, coming in to be touched.

On the cruise back to camp, Sheridan, by popular request, serenades us with his operatic song, adding to the soundscape of whale blows and waves.

After quickly changing into traveling clothes, we pack up into a van, leaving the camp. At first, we travel through the flat Vizcaíno plain landscape of sparse dwarf shrubs. A combination of extreme aridity and saline soils suppresses the vegetation.

Presently, we gain altitude as we progress eastward and inland. The landscape transforms to a dramatic cactus garden with tall cardons, shrubby chollas, and other cacti. We briefly get out of the van for a closer look and are greeted by a resident Cactus Wren, one of the largest wrens in the world.

At the mission oasis town of San Ignacio, we pause for a packed lunch of burritos and some local date bread. Crossing the peninsula, we reach the Sea of Cortez at Santa Rosalia and continue down the scenic coast. By late afternoon, we are back at our hotel with its most welcome hot showers.

March 12, 2017 | Loreto – USA

At our farewell breakfast, naturalist Roger Harris thanks everyone for coming on this excursion and in doing so supporting the conservation mission of the Oceanic Society. Then, we pack up, leave for the airport, and take our flight back to the States.

We have been privileged to have experienced nature still in a state not too different from when our species was not the dominant one on the planet.

Click here for more information about Oceanic Society's Baja: San Ignacio Lagoon and Sea of Cortez Expedition including itinerary, photos, video, and more.

© Jose Sanchez


Roger Harris is a long-time Oceanic Society naturalist with 30 years of experience working as a guide. In addition to working with Oceanic Society, Roger has frequently worked as a naturalist for Lindblad Expeditions and the National Audubon Society. As a naturalist he has led eco-tours in Honduras, Belize, Kenya, Great Barrier Reef, Galapagos, Baja California, and SE Alaska. Roger is also a professional conservation biologist specializing in endangered species, wetlands, and native habitat restoration. He earned a graduate degree in ornithology from U.C. Berkeley, and is both a NAUI diver and an expert world birder.


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