Ecuador’s famous archipelago is still a place where animals have the right of way, the exotic is accessible and the pages of a magazine come to life.

“Orca, orca, orca”, our guide Celso Montalvo shouted into the radio attached to his life vest, rapidly giving directions to the five other Zodiac rafts in our group. The tranquillity of dusk became charged with excitement as we surrounded the three killer whales – a mother and father who were teaching their baby how to hunt sea turtles off the coast of Isabela, the largest island in the Galápagos, an archipelago some 1,000km off the coast of Ecuador.

At the northern tip of Isabela, the frigid waters of the deep Equatorial Counter Current rise up along the western edge of the underwater Galápagos Platform, resulting in cool sea temperatures that occasionally attract whales and dolphins to the otherwise warm, arid  region.

A awe-induced hush fell over the group as the whales gracefully surfaced and dove  again, sometimes less than 3m from our 12-person raft, with only the click of a camera shutter interrupting the silence. In a whisper, our guide taught us to track the orcas’ path by following the pack of birds flying just above the surface as they feasted on the debris from each orca attack. Just minutes earlier, our group had been marvelling at the wealth of juvenile offspring living along Isabela’s Punta Vicente Roca cove -- young fur seals played in the waves and sea turtles surfaced like tiny floating rocks -- but as the sight of the orca hunt sunk in, a worry for the fate of those baby animals tainted the amazement of seeing killer whales in the wild. It was sights like these, presumably, that inspired Charles Darwin’s theory of evolution by natural selection when he visited the islands for five weeks in 1835.

It was day two of our voyage aboard the National Geographic Endeavor, a 96-passenger expedition ship that sails 10-day itineraries around the 13 major, and many smaller, islands that span the Equator.

The Endeavor, which is run as part of a partnership between two adventure tour companies, Lindblad Expeditions and National Geographic Expeditions, is one of the many vessels that house and ferry the nearly 180,000 visitors that come to the Galapagos Islands each year. Though tourism is good for the islands – it is the largest economic driver for the 23,000 people that live there – it also presents the ongoing dilemma of how to best protest a natural wonder that is threatened by the very source that funds its preservation – tourists.

In February 2012, less than two years after Unesco removed the Galápagos Islands from its list of endangered World Heritage sites, the Ecuadorian government passed new regulations that prevent any vessel from visiting the same site more than once within a 15-day period. According to the World Wildlife Foundation, by dispersing ship traffic throughout the region and decreasing tourist traffic at sites that are becoming too popular, the new regulations aim to ensure that the Galápagos’ fragile ecosystems – 97% of which are contained in strictly protected national park area – never become endangered again. It also means that visitors can never be sure which islands they will visit.

To remain compliant with the new laws, the Endeavour operates two seven-day sails around the region, alternating itineraries each week. Despite having some of the same markings as a cruise boat – there was a one-room spa, a two-treadmill gym and a small plunge pool at the back of the ship – the Endeavor is not a cruise. Maps lined the walls, charting our course and noting the wildlife we had seen; a library with wall-to-wall reference books covering topics from world history to oceanography commands a prime location on the bridge deck; and evenings were spent listening to scientific lectures on plate tectonics and the mating habits of land iguanas, given by the on-board naturalists certified by the Galápagos National Park.

The ship is also appropriately eco-conscious. Each state room is given two reusable water bottles in lieu of plastic ones; guests’ sandals are rinsed off each time they board so the sand can be returned to the beach to prevent erosion; and the boat is equipped with orange exterior lights, which are less attractive to bugs that standard fluorescent bulbs and help prevent the inter-island transportation of invasive species, meaning insects that follow the boat’s lights from one island to the other. Guests are even asked to keep their windows closed at night to help the same cause.

Wake up calls were often between 6 and 7 am, and each day was packed with early morning and evening hikes and a variety of afternoon water activities, including deep-water snorkelling, kayaking and spying the underwater world from a glass-bottom boat. Participation in any of the above was voluntary, sign-up sheets were in pencil and cancellation fees were non-existent – even for the massage treatments. But with each activity, passengers were increasingly unlikely to skip the next. Checking email and getting sleep could wait.

This spring expedition began with a 2km hike over lava boulders and muddy terrain on North Seymour Island, a nesting site for swallow-tailed gulls, blue-footed boobies and both magnificent and great frigate birds. Because of the season, many of the seabird species were courting each other – the blue-footed boobies were dancing, honking and whistling, and the male frigate birds were displaying balloon-like red pouches with pride, shaking them back and forth when a female passed.

In comparison, the next island, Rabida, was incredibly understated. While hundreds of massive sea birds glided in the warm air above North Seymour and arrogantly posed for photos, the tiny land birds that hid in Rabida’s dense vegetation were almost impossible to see, let alone photograph. But what Rabida lacked in bird life it more than made up for in unusual terrain, with jagged green peaks contrasted against dark red sands made from high iron oxide lava.

Rabida is also famous for being the focus of a large-scale eradication campaign, where destructive, introduced species such as rats are being strategically exterminated from the island to restore the original balanced ecosystem. Its success has been an example for similar projects around the archipelago.

On Fernandina, the youngest and most pristine island in the Galápagos, the terrain again shifted dramatically, with innumerable black lava flows flanking the island’s imposing 1,520m volcano, one of the most active in the world.

Along the shoreline, thousands of endemic marine iguanas were basking in the sun, their black skin making them nearly indistinguishable from the dark lava they lay on. Even more swam stealthily in the lagoon-like waters nearby. When just their heads popped above the surface, crowned at times with grey, crusty-looking spikes, it was clear why Darwin called them “imps of darkness”.

Throughout the trip we were reminded that keeping a healthy distance from the wildlife (the park rules say at least 2m) means there is little to fear. In the turquoise shallows off the coast of Santa Cruz, a large Galápagos shark swam away from us faster than we could follow it. In the dark blue waters near Fernandina, a baby sea lion spun circles around us, blowing bubbles and barrel rolling, torpedoing towards our snorkel masks and careening sideways just before impact. Pacific green sea tortoises, which can grow to be 84cm long, floated past us in slow motion and 30cm-tall penguins (the third smallest in the world and the only ones in the northern hemisphere) sped through the water like bullets. On land, massive reddish-yellow land iguanas lounged like tiny dragons across the path and the islands’ famous giant tortoises lumbered ever so slowly toward the group, welcoming us to their home. Before we even boarded the ship for the first time, we were greeted by giant sea lions lounging beneath the dock near the airport on Baltra Island. The wildlife was so abundant and so close that it almost felt staged, as through a director was standing in the wings, radioing directions to cue the flamingos’ entrance.

In late June, Lonesome George, a giant tortoise believed to be the last of his Pinta Island subspecies, passed away, shining an international spotlight on the need for continued conservation of the Galápagos Islands – an idea that reverberated in every hike, every snorkel and every conversation of our trip.

In an open letter, the International Union for Conservation of Nature wrote, ”More than just a symbol for the Galápagos, Lonesome George was a symbol of our global never-ending struggle to preserve the richness and diversity and beauty of the planet we inherited."

On the last night of our trip, we spent a night in the town of Puerto Baquerizo Moreno on San Cristobal Island, the capital of the Galápagos Islands. In the small town of 5,000 people, crowds flocked to the open-air bars, pick-up trucks ambled slowly down the main strip and children clamoured over a swing set, just steps from the beach. If it were not for the loud sneezes, snores and barks – it would have been a completely peaceful night. Because for every one person out in the harbour, there were at least two sea lions commanding a spot on the shore.

In the wild, we had only seen 10 to 20 sea lions together at one time, but in town, hundreds covered every centimetre of the beach along Shipwreck Bay. They lounged in the shallows beneath a waterslide clearly meant for children and they dominated the wooden boardwalk and stone piers, staking a claim on the best seaside property on the strip. We sat for a bit watching the kids playing in the park, and a young boy playing with a red ball caught my eye. He passed it back and forth with a friend, kicking it along the playground sand, until he missed it and it rolled right to the base of a park bench, where two 4ft sea lions were lounging. The little boy ran to the bench without hesitation, grabbed the ball and the sea lion barely stirred. Neither feared the other and both felt at home.

Of course, when we tried to gingerly walk past, the sea lion happily reminded us that this was his bench, as he rose up aggressively and began a bark that seemed to set off every other previously-slumbering sea lion. Clearly, even in the capital city, animals have the right of way and most of the humans are just visiting.