Galapagos Islands Itinerary

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Many visitors to the Galapagos Islands explore via multi-day cruises but quite a few of these enchanted isles and their underwater wonders are accessible via less expensive, independently arranged travel. You can save heaps by putting together your own Galapagos Islands itinerary

This do-it-yourself Galapagos Islands itinerary is relatively inexpensive and allows you to see all kinds of Galapagos Islands animals within easy reach of Isla Santa Cruz, Isla San Cristóbal and Isla Isabela.  

The Galapagos Islands is one of the most famous landmarks in Ecuador, which is one of the best countries to visit in South America for wildlife. There are flights from Quito and Guayaquil that service Isla Santa Cruz and Isla San Cristóbal (the easternmost island), with ferry services and comfortable inter-island flights connecting these two islands as well as the Galápagos’ largest island, Isla Isabela.

Galapagos Islands Itinerary

Day 1 – Isla Santa Cruz

You’ll see Galápagos sea lions hanging around the fish market in Puerto Ayora, the Galápagos’ largest, most populated town, but if you want to swim near them, Isla Santa Fe, about 20 kilometres southeast of Isla Santa Cruz, is a great choice for a day trip.

Day 2 – Isla Santa Fe

Galapagos Islands itinerary sea lion
Swimming with sea lions is one of the highlights of any Galapagos Islands itinerary.

After an initial snorkel alongside Santa Fe’s sheer rock walls, near schools of angelfish, you’ll cruise to a rocky area frequented by sea lions.

These mammals alternate between resting above the water and moving beneath it, scratching their bodies against underwater rocks and playing, sometimes pausing briefly to stare at your camera.

It’s quite a snorkelling adventure. 

Cost of an Isla Santa Fe day trip from Puerto Ayora, Isla Santa Cruz: about US$90 per person, including lunch and snorkelling gear.

A more expensive trip from Puerto Ayora is to Isla San Salvador (Santiago), which is often visited on an Isla Bartolomé day trip (approximately US$170 per person).

Day 3 – Isla San Cristobal 

the galapagos islands wildlife
Your Galapagos Islands itinerary will showcase a range of birds and wildlife.

On the northern end of Puerto Baquerizo Moreno, the Galápagos’ second most populated town, is the Galápagos National Park Interpretation Centre.

From the centre, a five-kilometre loop trail leads further north towards Frigatebird Hill (Cerro Tijeratas), a site where two species of frigatebird nest in the same colony.

At the base of this hill is a protected, shallow cove, home to a colony of sea lions.

Snorkelling adventure

The sea lions love lounging on the walkway leading to this snorkelling spot, so you may have to wait awhile for them to move.

If so, be patient – you’ll get there eventually.

sea lion
Getting close to sea lions is something you will do easily on this Galapagos Islands itinerary.

When you do enter these calm, 3 to 5m waters, you might encounter a green turtle, swimming gracefully or resting.

galapagos island snorkelling 708
Another Galapagos Islands itinerary highlight is swimming with sea turtles.

You might also observe some playful young sea lions, frolicking twenty metres or so from the resting adults in their colony.

Playful sea lions in the water in Galapagos Islands
These playful sea lions are fun to watch in the Galapagos Islands.

Refrain from venturing too close to them, though as adult males, in particular, can be quite territorial and aggressive.

Cost from Puerto Baquerizo Moreno, Isla San Cristobal: free. (BYO snorkel gear)

A more expensive choice from Puerto Baquerizo Moreno: a day trip to Kicker Rock (approximately US$80 per person).

Day 4 – Isla Isabela 

Puerto Villamil
Puerto Villamil is another snorkelling spot to put on your Galapagos Islands itinerary.

About a kilometre from Isla Isabela’s main town, Puerto Villamil, is a harbour and jetty.

The smaller walkway running alongside it is the perfect launching point for a fantastic, inexpensive snorkelling adventure.

It’s a great place to go when visiting the Galapagos Islands.

Marine iguanas lounge on the walkway, and also swim in the harbour; while they’re interesting to observe, they’re not the main species you’ll probably encounter in the water, though.

The highlight of this snorkelling spot – as with the other places we’ve mentioned – are the sea lions.

You might observe one or two … 

sea lion in the water at Isla Isabela
Isla Isabela is another Galapagos Island itinerary spot to snorkel with sea lions.

…or possibly a larger group, playing and occasionally pausing to check out you and your camera.

Snorkelling adventure

Also keep an eye out for Galápagos penguins, which also zip past occasionally.

Galapagos Islands itinerary - snorkel with penguins
Snorkelling with penguins is a nice surprise on this Galapagos Islands itinerary.

Cost from Puerto Villamil, Isla Isabela: free (BYO snorkelling gear)

A more expensive choice from Puerto Villamil, Isla Isabela: a day trip to Los Tuneles (approx. US$60 per person)

Inspired to visit the Galapagos Islands? Here’s what you need to pack for your Galapagos trip.

Also, check out this video showcasing a couple of these snorkelling spots as well as a few others.

Galapagos Islands Itinerary
Galapagos Islands Itinerary
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Kara Murphy
I’m a travel photojournalist, based on Brisbane’s bayside in Queensland, Australia, and specialising in underwater and other outdoor adventures. Some of my favourite underwater experiences have happened close to home – on Moreton Bay and, a bit further north, on the southern Great Barrier Reef.You can find my work in publications such as ShowBoats International, Australian Geographic, Dockwalk, and Go Camping & 4WD Adventures, and I also create short videos for my YouTube channel. Awards 2014 winner Diver(s) category, Cairns Underwater Film Festival 2013 Australian Society of Travel Writers finalist for Best Australian Story Under 1000 Words