Galapagos Island Hopping : Plan Your Own Adventure

Created by Colleen Sims * 14 June 2023 * Updated 15 August 2023

I wanted to see Frigate Birds when we visited the Galapagos; I wasn't disappointed on North Seymour
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We travelled independently through the Galapagos Islands; and we island hopped. The Galapagos Islands are a true natural paradise, located off the coast of Ecuador. This amazing archipelago is the stuff of Attenborough documentaries and known for their exotic wildlife, pristine beaches, and stunning landscapes.

Unfortunately, the Galapagos Islands are also associated with high prices and lots of folks think they are inaccessible for most budgets.

But we discovered a way of travelling to Galapagos on a smaller budget. We hopped between the three main islands; here’s what we did to enjoy the Galapagos Islands without breaking the bank.

Why We Chose the Galapagos?

The Galapagos were on Gerry’s wish list; actually giant tortoises on the Galapagos have always been on his list. As a young chap we was fascinated by the evolution of the islands and yearned to see the tortoises up close.

We travelled from Europe and it took us four flights to get there. We flew into Quito from Amsterdam with KLM but you can also fly into Guayaquil if it’s easier for your flight. We spent the night in Quito, although we saw very little as we arrived late and left early but our overnight stay was fabulous and I would thoroughly recommend the simple Quito Eco Lodge; they could not have been more helpful! If you’re looking for a little more frills there is a Holiday Inn very close to the airport.

Travelling Independently on Galapagos

There are two ways to explore Galapagos. You can take a cruise and spend your time visiting some of the more remote areas of the Galapagos. To make the most of your cruise I think you would need a 6 or 8 day cruise; shorter cruises don’t offer much more than island hopping.

TOP TIP : if you plan to cruise and are waiting for a last-minute bargain make sure you plan your travel days accordingly. Cruises start from different islands on different days and our flights made it difficult to find suitable last minute cruise. So search cruises in advance of booking your flights to ensure that you’re in the right place at the right time.

I loved the idea of a cruise but it would have stretched our budget too far and so island hopping was a natural choice for us. And now, having finished our holiday, I actually feel the island hopping was the perfect choice for us.

Galapagos Islands Map on display at the Charles Darwin Centre on Santa Cruz Island

Island Hopping the Galapagos

There are three inhabited islands, each offer something different and each are easily accessible to independent travellers. If you are planning a trip to Galapagos then Santa Cruz would be your first and main choice if you can only choose one island. There are more excursions available from Santa Cruz.

We choose to visit all three of the inhabited islands and do not for a moment regret that choice. Our only regret was time. If you have time then do stay longer. See more. Explore! We could have easily added at least a week or two to our trip and it would not have cost a huge amount more. There are so many things to see, take your time and enjoy all that the islands have to offer.

Emtebe Flights from isabela to San Cristobel; a quick way to island hop in the Galapagos

Santa Cruz Island, Galapagos

Santa Cruz Island is one of the central islands in the Galapagos archipelago. It is the second-largest island and has a population of 18,000.There are several day tours that you can take from Santa Cruz and well as plenty of activities on the doorstep.

Puerto Ayora

This is the largest town on the Galapagos and the main hub for tourism, Here you’ll find a range of accommodation options, restaurants, shops, and visitor sites.

Charles Darwin Research Station

The Charles Darwin Centre is an easy walk from the main harbour at Puerto Ayora. You can visit the centre independently, and jump on a guided tour of the breeding centre for 10$ (arranged at the entrance). The research station is crucial for scientific research, conservation, and environmental education in the Galapagos. It focuses on the preservation of the islands’ unique ecosystems and the protection of endemic species. There is a small cafe here for refreshments and drinks as well as a beach where you can snorkel.

There’s very little shade here so make sure you have a hat and sunscreen during your visit.

Tortuga Bay

This is a pristine white-sand beach located just out of Puerto Ayora. It’s known for its crystal-clear turquoise waters and perfect for snorkeling. Expect to see lots of marine iguanas, sea turtles and seals.

There is an ‘entrance’ to the beach and it closes early. We arrived at just after 3:30pm and were not allowed access that day. There is a 2km walk to the beach and the ‘guide’ felt that it was too late to walk there and back and return in time for closing at 5:30pm. So go in the morning! Take everything you’ll need as there are no services on the beach, and it is exposed with little shade. But – this is a must see beach whilst on Santa Cruz.

A huge male sealion blocked the access to our island hopping zodiac boat on Bartolome, Galapagos

Los Gemelos

Los Gemelos, are known as the Galapagos twin craters, and form part of the green forested area of the Highlands on Isla Santa Cruz. These enormous sinkholes were formed when lava tunels beneath the land collapsed. In places these sunken craters are 230m deep.

Our driver stopped here en-route from the airport. It was an easy stop and we simply followed the marked trail to discover the joint crater circuits. We actually got caught up in a group of Americans and took advantage of their botanist guide as he explained the flora and fauna and literally pointed out the birds and the bees.

El Chato Giant Tortoise Reserve

This was ab absolute must for us. Gerry wanted to see Giant Tortoises. Again we opted to visit here en-route to our accommodation at Puerto Ayora; it’s on the way and it would save time.

El Chato is a Giant Tortoise reserve. At the reserve we were handed over to another botanist guide, we swapped our shoes for wellington boots and were led off into the reserve.

All around us wandering free are Giant Galapagos Tortoises. These are the land eating short neck variety; on other islands there are long necked tree eating tortoises. Our guide told us that tortoises floated to the islands, across the Pacific from South America maybe 5 million years ago; who knew that tortoises could float! They are long lived creatures, one of the tortoise that Darwin took back with him only died in 2006!

Giant Tortoise on Santa Cruz; part of our island hopping Galapagos adventure

An interesting fun fact : males are bigger and their shells are quite rough. Females are smaller and their shells tend to be smooth, sandpapered like a nail file during the mating process; the older the lady, the smoother her shell!

We were allowed to wander freely after our guided tour but you must at all times stay at least 2m from any creature, no feeding them and no flash photography. Gerry beamed for about 2 hours.

You can also visit the Lava Tunnels at El Chato as part of your tour. And we stayed for lunch after.

Isabela Island, Galapagos

Isabela Island is the largest island in the Galapagos archipelago, and apart from the wildlife it’s known for for its volcanic formations. Isabela Island was formed by six shield volcanoes, and is one of the most volcanically active places in the world. Whilst it maybe the largest island is it less populated than Santa Cruz and has a very laid back atmosphere.

We took the inter-island ferry to Isabela; it’s generally a rough crossing and takes just over 2 hours so not ideal if you don’t have good sea legs. There is also the option of inter-island flights with Entebe.

We had bad weather on our Ferry crossing from Santa Cruz to Isabela; no snorkelling for us on this island!

Sierra Negra Volcano

We were drawn to Isabela because we wanted to hike the Sierra Negra Volcano. Sierra Negra is one of the most active volcanoes in the Galapagos, and its caldera is one of the largest in the world.

This hike was incredible. We had awful weather but would not have missed this day for anything!


Isabela is a great place for snorkelling. Tintoreras is a small group of islets near the main town of Puerto Villamil. It offers opportunities to see a diverse range of marine life, including marine iguanas, sea lions, rays, and sharks. Sadly the weather was really bad when we were here and this activity wasn’t available to us.

Concha Perla

Another favourite snorkelling spot on the island is the Concha de Perla; known for the quality of snorkelling. Usually a calm shallow bay, with crystal clear waters, and a pontoon for easy access to the water, which is teaming with marine life it’s a great free activity. Located just beside the port it’s also just a few minutes walk from the centre of Puerto Villamil.

Sadly for us again the weather made this impossible and we never got to experience this glorious mini-adventure.

even the awful weather didn't stop us loving our hike on Isabela Island to the Sierra Negra crater and lava field

Arnaldo Tupiza Tortoise Breeding Centre

The Tortoise Breeding Center of Isabela is located 1.5 km from Puerto Villamil and you can easily walk from town. Opened in 1995, in response to a major fire on Isabela that threatened the tortoise habitat the centre includes breeding groups of tortoises and returning young for return to the wild. It houses approximately 70 breeding adults and produces approximately 250 babies a year.

Wall of Tears (Muro de las Lágrimas)

We had limited time on Isabela and one regret was not allowing more time on each island. Getting to the Galapagos is expensive but staying on the island is cheaper. The Wall of Tears dates back to the time when Isabela Island was used as a penal colony. Prisoners were forced to construct this wall using volcanic rocks.

San Cristobal Island, Galapagos

San Cristóbal Island was one of our favourite places. It is not as laid back as Isabela and not quite so touristy as Santa Cruz. It is one of the easternmost island and one of the older islands. San Cristóbal also has an international airport; which we could walk to from our accommodation.

To save time we took the small inter-island flight from Isabela; it was a great choice!

Sealions sunbathing on the beach on San Cristobel in the Galapagos

Puerto Baquerizo Moreno

Puerto Baquerizo Moreno is a vibrant town with a large array of accommodation, restaurants, shops, and services for visitors. There is also great promenade where you can spot sealions, pelican, iguana and other wildlife sunbathing on the beaches!

La Lobería

This is the most popular beach for observing sea lions in their natural habitat. You can also snorkel, and swim and observe plenty of other marine life such as turtles and marine iguanas.

El Junco Lake

El Junco, in the highlands of San Cristobal is the only freshwater lake in the Galapagos Islands. The lake is an ancient volcanic crater, and popular with Frigate birds. The site is easily reached by taxi and you can hike around the lake (although it can get a bit muddy). If you have time this is a great place to explore and provides a different scenic viewpoint for visitors.

Galapaguera de Cerro Colorado

If you miss the tortoise breeding centre on other islands then you can also visit one here. The centre is dedicated to the conservation and breeding of Galapagos giant tortoises and you can observe tortoises at different stages of development.

Galapagos Entry Requirements

When travelling to the Galapagos there are several rules you’ll need to follow. You are required to complete an Island Tourist Entrance Visas or INGALA transit card at the airport. And, your bags must be biologically scanned and sealed to ensure that you are not carrying prohibitive items onto the islands.

I would recommend allowing an extra hour at the airport as there are queues for each of these actions. At Quito the INGALA desk is very near the entrance. We joined the queue and the process was simple. They spoke excellent English; do have your passport, tickets and travel documents ready along with the fee (20$ in May 2023). You’ll be given your transit card which you must keep until you exit Galapagos. After this you join another queue, across the hall. It’s a little obscure as there is a door into another room, but anyone will direct you. This is where your bag will be biologically scanned. Once this is done the luggage is tagged and cannot be reopened.

Once you have completed these two stages , you then follow standard airport security in the same way as any other international airport.

Ecuador to Galapagos: Quito to Guayaquil to Baltra

Flights from Quito generally go via Guayaquil, you don’t need to exit the plane, but there will be a 30-40 minute pause on the plane whilst folks leave and new folks arrive.

We flew out of Quito looking out at the volcanic landscape of the Andes; we counted at least 5 active volcanos, belching grey smoke above the clouds. As we got on the plane a gentle mist was pumped through the cabin, and later before landing the crew went through the plane spraying all the hand luggage; apparently non-toxic!

looking down at the active volcano flying from Quito to the Galapagos

Baltra or San Cristobal?

When flying into the Galapagos you have the choice of two international airports. We opted to fly into Baltra and as we were island hopping we flew out of San Cristobal. Baltra is a tiny island and is the airport you’ll choose to visit the main island of Santa Cruz.

Once you land you’ll need to go through a second immigration process and pay another fee for your entry visa or National Park fee; 100$ each in May 2023. But the process is simple and you are guided every step of the way.

How to Get from Baltra to Santa Cruz

We had arranged to be met; our accommodation had arranged this but it’s not needed. Outside the airport there is a tourist bus that takes you to the Baltra Ferry.

Baltra is the airport island. All visitors must take the bus to the Ferry port. There is a constant ferry running from Baltra to mainland Santa Cruz crossing the Itabaca Channel . Cost is just a few dollars and again very straightforward; you are guided onto the bus and again onto the ferry. Regardless of having a private transfer you will need to follow this process. Our entire journey took perhaps no more than 30 minutes and if we had any concerns they were unfounded; this journey is really very simple.

Once we arrived on Santa Cruz our driver met us. We had pre-arranged a driver as we wanted to make a few side trips en route to Puerto Ayora (the main centre on Santa Cruz). If you’d rather go direct to your accommodation there are regular buses running from the port and there is no need to pre-book.

Marine Iguana on North Seymour Island Galapagos

Island Hop from Santa Cruz to Isabela or San Cristobal

Travelling between islands is straightforward. You can choose the inter-island ferries or you can opt for the more expensive inter-island flights.

We took the ferry from Santa Cruz to Isabela. It was a rough crossing and several people were sea-sick. The journey took 2 hours and in bad weather it’s not for the feint hearted BUT the ferries run everyday and the cost is around 35$ so it’s a really inexpensive way of travelling.

We moved on to San Cristobal from Isabela Island and you can either take a ferry back to Santa Cruz and then take another ferry to San Cristobal or fly. We didn’t wish to waste a day travelling between the two islands so we opted for the flight. It was a great choice and we loved the experience. It was quick and we saw the islands from the air. Emtebe is the operator and you can book your seats online.

Island Tours

From each island we opted to take day tours. There are limits to the islands you can visit and the tours are expensive; expect to pay around 280$ per day. However, we loved our day trips, they were the highlight of the holiday and if we could have stayed longer we would have opted for a few more tours!

There are a great many tour operators and travel agents selling day tours. However, there are a limited number of boats and so most agents are all selling the same tours.

Santiago Island from the hike to the top of Bartolome Island; a day tour from Santa Cruz Island

I spent hours pouring over different trips to make the most of our budget and to ensure we managed to visit the islands with the wildlife we were seeking. In the end we booked all of our tours through Guiding Galapagos and we were not disappointed. They were less expensive than some and more expensive than others but we could arrange everything in advance, they have an excellent reputation and everything was organised and paid for before we left home.

If you prefer you can make your plans once you arrive but with limited time we wanted to ensure we could visit the islands on our wish list.

Top Tip : Do lots of research on the different islands and the different tours available. Each island offers something different. I knew that we wanted to see Frigates, Boobies and Albatross so I researched where and when we could see these. If you wish to dive or see sharks then you will want to visit islands that offer this. We wanted to snorkel but it wasn’t the only factor for us; if you want lots of snorkelling you’d choose a different tour. We wanted to walk around the islands so this was important for us; others may not wish to hike so again, you’d choose differently. Armed with this research I contacted Guiding Galapagos with my wish list. Their prices for each tour were very competitive and I was happy to book all of our trips with them. They also choose good quality boats, which is super important and they have insider knowledge! But… do your research first.

Tours from Santa Cruz

  • North Seymour Island
  • Bartolome Island         
  • South Plazas Island     
  • Santa Fe Island       
  • Pinzon
  • Floreana

We visited North Seymour and Bartolome but if we had time I wish we had also visted South Plazas, Pinzon and even Floreana

Tours from Isabela

Isabela is all about volcanoes but there are other options too.

  • Sierra Negra Volcano Hike
  • Los Tuneles Snorkeling Tour
  • Tintoreras Islet
  • Isla Tortuga

Do the hike! we had awful weather but we loved this day. I also would have loved to visit Fernandina but it is only accessible on longer cruises.

Tours from San Cristobal

Another big regret was time on San Cristobal. We came for our tour to Espanola but there is so much more to see and do.

  • Española
  • Kicker Rock
  • Punta Pitt
  • 360 Island Tour
  • Isla Lobos

Day tours when island hopping are not a cheap option but they are still less expensive than a full cruise. We loved all of our tours and in the end felt that they were worth the cost. We visited some of the more distant islands, we loved the journeys and learned so much from the guides. We were collected from and returned to our hotels, we were fed and there was always a chance to snorkel and hike.

If we were planning this trip again we would have stayed with our island hopping travel but would have allowed more time on each island and we would have taken 3 or 4 more day tours. Overall we feel this would have still been better value than a cruise and offered us a huge variety of activities!

Snorkelling off the beach on the North Seymour Island in the Galapagos

The Last Word : Is it Worth Island Hopping in the Galapagos?

Absolutely! We’re in our 60s and we found it easy to plan our trip to the Galapagos.

We booked our flights to and from Galapagos direct on the LATAM website and whilst I researched many different tours I opted to go with Guiding Galapagos to book our day trips. They were less expensive than many but offered excellent communication whilst on the island, all we had to do was be in the right place for our pick-ups.

We booked our accommodation through and our own island-hop flights via Emtebe. If you can shop online then you can save yourself a great deal by organising your own visit. Island hopping is a great way to see each island at your own pace. My one regret was not allowing more time on each island!

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