A heron stands just behind me on the trail, his head cocked. Unimpressed, he considers the line of people on the path observing a cormorant’s nest opposite him. With a couple more little jerks of his head, he makes a decision and walks right between me and another traveller, nearly stepping on my foot.

Clearly, he doesn’t need to mind where he is going. I, however, have strict instructions not to step off the path, which is just unaltered terrain between a few scattered posts.

“The policy of the Galápagos National Park is to leave everything as natural as possible,” says my guide. There are no docks, pit toilets, garbage receptacles, or park offices. With the exception of an occasional trail post, the land looks completely untouched. But that is an illusion; although 97 percent of the land area and most of its waters are protected, the islands are constantly under threat. Their history of geographical isolation is trumped by human population growth, introduced species, and illegal fishing and poaching. This trip of a lifetime could potentially be the trip of my generation.

The Galápagos Archipelago, made up of 14 islands and over 120 islets and rocks, straddles the equator more than 900 kilometres off the coast of Ecuador. Volcanoes formed the islands millions of years ago, and though conditions are often quite harsh—many of the islands are mostly rock with scraggly plant life and no fresh water—life has adapted and flourished in isolation from the rest of the world. Forty percent of the roughly 5,000 plant and animal species here are unique to these islands.

I am travelling aboard a 40-person yacht through the archipelago. Typically, I cringe at the thought of a cruise, but this expedition does not feature conga lines or lounge acts. Wake-up call is at 6 a.m. for shore excursions. Daily activities include hiking and snorkelling, swimming, kayaking, and glass-bottomed-boat tours. There are presentations on evolution, plants and animals, geology, and Charles Darwin.

My group arrives at Hood Island in a rubber launch called a panga, and we slip over the sides into knee-deep water. As I ogle the so-called wild animals, they ogle me with curiosity. What on earth are these humans doing on this island, so ill-adapted to the strong sun, hopelessly vulnerable to the dearth of fresh water and food? Only the crabs seem to be cautious, scuttling away when I am finally within a quick grab of their orange-and-blue armour.

Maybe they’re the smart ones. The human population in the islands is estimated at over 30,000, many of them here illegally. Over 120,000 tourists visited in 2006, and the authorities may set a lower limit as concern grows about the negative impact.

We are warned not to touch any of the animals, but the animals have no such rules. Finches land on shoulders. Sea lions flop across the sand to sniff us out. Perhaps their mothers should have warned them; my scent on an infant could be a death sentence, as mothers recognize their offspring by smell. A pup wanders the beach wailing in distress while its mother is probably out searching for food. In the hour we spend at this location, only one female approaches and—as if demonstrating what the naturalist has just told us—brushes along the pup’s fur with her nose. Then she continues down the beach, leaving the pup to wail. We humans look on hoping that what will probably happen, won’t. Here and there throughout our hikes I have seen tiny carcasses like macabre balloons shrivelled up in the harsh sun.

“Doesn’t the park save the animals?” someone asks.

The answer is no. Sometimes, as with a healthy sea lion population, our human commitment to preservation requires inaction; other times, as in the case of the giant tortoise, it requires an effort to reverse past abuses.

We spend an afternoon at the Charles Darwin Research Station, which operates a tortoise farm on Santa Cruz Island. There were once 15 subspecies of giant tortoises in the Galápagos Islands, and four of those have now been lost. The lumbering reptiles were easily hunted for food and their shells, and even scientists once wanted them in museums. Part of the CDRS’s work is the eradication of invasive species. Goats and rats are just a couple of threats to the native animal population.

The celebrity of the CDRS is Lonesome George, the last known example of the Pinta subspecies. That thought sticks in my head: this creature is gone forever one or two generations from now. Recent genetic samples from Isabela Island have given some hope that there may be another Pinta tortoise there, but even so, the odds of survival for this species are abysmal.

A tanker that ran aground off San Cristobal in 2001 showed how much damage can be done with just a moment’s carelessness. Though it was a “minor” spill of diesel, which is less toxic than crude oil and evaporates quickly, over 60 percent of the marine iguanas on nearby Santa Fe were dead within a month. The guide stops to show us this odd reptile that dives for its meals of algae. They have adapted to drink seawater and expel salt from their bodies by sneezing, which my naturalist jokingly refers to as “snot rocketing”.

For my last excursion I opt for time in a kayak while others take a panga tour of the shoreline along Floreana Island. It is a rare opportunity to explore by myself. I stop paddling and sit still as the motor of the panga fades to a distant hum. I look around at the small bay, at the volcanic ash cones like perfect mountains beyond, and I listen to wind and waves. Something moves and I glance around at the rocks. I see them all staring right back at me: sea turtles. My heart leaps and my hand instinctively goes for my camera. But they are nothing more than little heads like periscopes poking through the smooth surface of the sea in a circle around me, curious about that bright-yellow boat with the odd fins. No camera captures the feeling of mutual observation. I raise the paddle and seven rocks disappear.

Moments later I find a playful sea lion. She’s nosing along the shallows in search of food, and I dip my waterproof camera into the water to try to get a shot of her blowing bubbles into the lens. She glides into a smaller inlet that will soon become cut off from the sea as the tide slips from the sands and the sharp rocks rise up around it like fortifications. I rush to see before it’s too late.

ACCESS: In the Galápagos, what you see depends on when you go. April and May offer good visibility for snorkellers and the best weather. Blue-footed boobies begin courting in May, sea lions start giving birth in August, and giant tortoise eggs begin hatching in December. Galápagos penguins are most active from May through September. High season (and higher prices) runs mid June through mid September and November through April.

Tour prices start around $540 for four-day, no-frills tours, but I recommend seven days minimum. (Half of a four-day trip is arrival and departure and just settling in.) The national-park fee is not typically included in the price and is US$100.

Avalon Waterways and Metropolitan Touring sponsored the writer’s trip. Avalon offers nine- and 14-day trips, which include some ground touring in Ecuador, starting at US$3,539. Cruise only runs $1,549 and $5,059 respectively. Starting point for cruises is Santa Cruz Island. One must fly from Ecuador to the Galápagos out of Guayaquil or via Guayaquil from Quito. See www.avalonwaterways.com .