Galapagos Island Hopping : Affordable Fabulous DIY Tour

Created by Colleen Sims | Updated : 14 June 2023 | ,

I thought you could only visit the Galapagos as part of a tour. And specialists tours can be pricey. I did some research and the more I read, the more I realised that we could plan our own visit for a fraction of the cost.

We travelled independently through Galapagos and we island hopped. We visited seven of the islands and our only regret was that we didn’t stay longer.

The Galapagos Islands are associated with high prices and most folks think that they are inaccessible but we discovered that the islands are way more affordable that folks realise. And it’s possible to organise your own Galapagos adventure.

I wanted to see Frigate Birds when we visited the Galapagos Island Hopping; I wasn't disappointed on North Seymour.  This beautiful Frigate has his red chest fully puffed.

Galapagos : Cruise or Island Hopping?

We had no idea if we could organise our own DIY tour but learned that not only is it possible, in the end we felt it suited us better and for a lower cost.

We travelled across the Galapagos Islands, albeit we sacrificed some of the luxuries you’d get on a cruise. We hopped between the three main islands and loved every minute.

If like us you yearn to visit these stunning islands but think you can’t afford it, then think again. Our only regret is that we didn’t stay longer.

Colleen and Gerry, sailing to Bartolome Island during our Galapagos Island Hopping Adventure.  We loved every minute of this amazing day

Why Visit The Galapagos?

Is there anyone on the planet who has not heard of these incredible islands?

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 and unique wildlife, pristine beaches and stunning landscapes.

It was here, on a visit to the islands, that Charles Darwin gained his understanding of the evolutionary process and started his work on the origin of species.

We learned during our visit that climate change and polluted seas are already impacting on the islands and changing their fragile ecology. In an attempt to preserve the islands, some are no longer accessible to tourists and others have limited access. It’s entirely possible that more restrictions will be introduced.

If the Galapagos Islands have been on your wish list for a while then I suggest you plan your visit sooner rather than later.

pelicans wander freely around the fish market in the main town on Santa Cruz, Galapagos

How To Reach The Galapagos Islands

We travelled from Europe and it took us four flights to reach the Galapagos Islands.

To reach the Galapagos you must first land in Ecuador. We flew into Quito Airport at night but you can also fly into Guayaquil; these days Guayaquil is not a place you’d want to stay overnight so I’d recommend Quito.

Quito Eco Lodge

We spent the night in Quito, although we saw very little as we arrived late and left early.

We stayed at a very simple homestay and the owners could not have been more helpful; including collecting us and returning us to the airport.

  • Close to the airport
  • Simple accommodation but everything you need
  • Super helpful host who arranged everything for us; including a SIM

Holiday Inn

We had some concerns arriving in Quito. It does have a few safety concerns. We were very happy with our homestay but If you’re looking for a few more frills this Holiday Inn very close to the airport.

  • International chain with familiar services
  • Only Minutes from the airport
  • Even has a swimming pool to shake off the jetlag

Top Tip : Arrange your airport taxi in advance of your arrival. I recommend that you arrange transport with your hotel and certainly through a trusted source. We would not recommend UBER on this occasion.

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 TCT Transit Control Card at the airport (when we travelled this was called the INGALA card). Your bags must also be biologically scanned and sealed to ensure that you are not carrying prohibitive items onto the islands.

I would recommend allowing at least 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. Just join the queue and the process is simple and 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 a transit card which you must keep until you’ve completely exited the Galapagos Islands.

After the INGALA desk you need to join another queue, across the main hall. It’s a little obscure as there is a kind of non-descript door leading into the scanning room; if confused anyone will direct you. Here your bag will be biologically scanned. You are not allowed to take animals, seeds or plants to Galapagos. Once scanned luggage is tagged and cannot be reopened until you arrive on the islands.

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

galapagos espagnola tour

Ecuador to Galapagos via Quito and Guayaquil

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 were a little surprised and confused when we landed at Guayaquil but you don’t need to do anything but sit and wait.

Expect a gentle mist to be pumped through the cabin before you land and expect the crew to go through the plane spraying luggage; apparently it’s all non-toxic.

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

Galapagos Island Airports

When planning our visit I was most confused by which airports we would use on the Galapagos Islands. My main confusion stemmed from Santa Cruz airport being located on the tiny neighbouring island of Baltra. There’s nothing on Baltra except for the Santa Cruz airport. And to make it even more confusing the Santa Cruz/Baltra airport is called Seymour; another Galapagos Island.

For International flights you arrive at either :

We flew from Ecuador with LATAM and we were really happy with their service. We used them again in Peru and never once had a problem. Use SKYSCANNER to check all flight availability and prices.

Top Tip : If you are island hopping the try to plan your arrival on one island and depart from another. We arrived on Santa Cruz (Baltra) but ended our visit on San Cristobal. This will save you a day of travelling between islands and there was very little difference in the flight cost.

iguanas sunning themselves on a wall beside the beach on Isabela island Galapagos

Arriving On Galapagos

We landed first on Baltra as we planned to explore Santa Cruz first. It was quite a surreal moment for us landing and walking off the plane knowing we’d finally reached the Galapagos Islands!

Once you land remember that there will be a second immigration process and you will pay another fee for your entry visa or National Park fee; 100$ each in May 2023. The process is simple and you are guided every step of the way.

You should expect to pay a fee every time you island hop.

Gerry looking so happy having just arrived in the Galapagos at Seymore Airport on Baltra, Santa Cruz

Island Hop and Cruise : Last Minute Bargains

As you know there are two ways to explore Galapagos. You can cruise. Longer cruises (6+ days) do allow you to visit some of the more remote islands but the shorter cruises tend to visit locations that you an easily reach on day trips.

If not cruising then you can island hop and a surprising number of people do it. And it’s easy to arrange independently. There are many day tours to other islands and lots of free things to do; you’ll not be short of places to explore.

We did consider mixing things up a little and taking a short cruise just for the experience of cruising in addition to our island-hopping. There are last minute bargains to be had but our dates just didn’t match the cruise departure dates. So we never took a 3 or 4 day cruise, I don’t feel we missed out but it’s an option for some.

TOP TIP : If you would like a 3 or 4 day last minute cruise then make sure that you plan your travel days accordingly. Cruises start from different islands on different days of the week and our days/dates didn’t match and made it impossible to find last minute bargain. Search the cruises in advance of booking (the dates are fixed ahead) then book your flights to ensure that you’re in the right place at the right time.

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

Which Islands To Hop To and From On Galapagos

There are three main inhabited islands, each offer something different and is easily accessible to independent travellers.

  • Santa Cruz : Puerto Ayora is the biggest town with a population of around 10,000.
  • Isabela : Puerto Villamil is the main town with a population of around 2000.
  • San Cristobal : Puerto Baquerizo Moreno is the main town and has a population of around 5,600.

If you are planning a trip to Galapagos then Santa Cruz would be your main choice. And if time is short and you can only choose one island then Santa Cruz is a good option. There are more excursions available from Santa Cruz and transport links are easy.

We choose to visit all three of these islands and do not for one moment regret that choice. Our only regret was time. If you have time then stay longer. Go and see more and explore more.

We could have easily added a week or two to our trip and it would not have cost much more; especially if you look for more simple accommodation. There are so many things to see; take your time and enjoy all that the islands have to offer.

sunset san cristolbal galapagos

Santa Cruz Island

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 as well as plenty of free activities.

Puerto Ayora

This is the largest town on the Galapagos and the main hub for tourism, Here you’ll find a range of accommodation, 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 station is crucial for scientific research, conservation and environmental education on the Galapagos. It focuses on the preservation of the islands’ unique ecosystems and the protection of endemic species.

There is a small café 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 snorkelling. 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.

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. These enormous sinkholes were formed when lava tunnels 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 an absolute must for us. Gerry wanted to see Giant Tortoises. Again we opted to visit en-route from the airport; it’s on the way and it saved time and money.

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

All around, wandering free are Giant Galapagos Tortoises. These are the short neck variety; on other islands there are long necked tortoises. We learned that tortoises floated to the islands across the Pacific from South America up to 5 million years ago; who knew that tortoises could float!

These are long lived creatures, one of the tortoise that Darwin took back with him only died in 2006.

We were allowed to wander freely around the park after our guided tour but you must stay at least 2m from any creature, with no feeding and no flash photography.

You can also visit the Lava Tunnels at El Chato as part of your tour. We’d recommend this as it was fascinating. There is also a restaurant on site and we stayed for lunch afterwards.

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.

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

Day Tours from Santa Cruz Island

We visited North Seymour and Bartolome and loved these but if we had time I would have visited South Plazas, Pinzon and Floreana. Each island offers something different.

Top Tip : Do allow time on Santa Cruz too s well as time for tours. Charles Darwin Centre and Tortuga Bay are free and you MUST visit both at least once.

our boat in the water around Bartolome Island, one of our day tours when visiting the Galapagos Islands

Isabela Island

Isabela Island is the largest island in the Galapagos archipelago and apart from the wildlife it’s known 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.

Colleen and Gerry at Isabela island airport waiting to board our tiny plane to fly us to San Cristobal in the Galapagos

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 de 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 and is a great free activity. Located beside the port it’s 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 Centre 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 to the wild. It houses approximately 70 breeding adults and produces approximately 250 babies a year.

Wall of Tears (Muro de las Lágrimas)

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.

Day Tours from Isabela Island

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

If you like a walk then 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.

Bad weather stopped us doing a few days of exploring which is another reason to allow plenty of time. You can snorkel from the beach on Isabela for free but the weather was just awful.

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

San Cristobal Island

San Cristóbal Island was one of our favourite places. It is not as laid back as Isabela and not quite as touristy as Santa Cruz. It is one of the eastern most 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. There is also a 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.

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.

Day Tours from San Cristobal Island

Another big regret was time on San Cristobal. We came for our tour to Espanola but there is so much more to see. But we LOVED Espanola!

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 40$ so it’s a really inexpensive way of travelling. You can fly but of course it adds cost. We don’t regret the crossing but we have good sea legs.

We moved on to San Cristobal from Isabela Island. From Isabela we had a choice.

  • Take a ferry back to Santa Cruz and then take another ferry to San Cristobal
  • 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. We saw the islands from the air which was also amazing. Emtebe is the operator and you can book your seats online.

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

Galapagos Island Hopping : Booking Day Tours

From each island we opted to take day tours. There are limits to the islands that you can visit when not cruising but honestly this wasn’t an issue for us. I’ve listed above the islands and tours that you can take.

The tours are expensive; expect to pay around 300$ or more per person. I was so convinced that this had to be wrong that I spent days and days searching online for alternatives. Don’t waste your time. This is the cost.

Some tours cost less and if budget is an issue then choose the less expensive tours; honestly the islands are so amazing you’ll still have a great time!

You can get cheaper tours if you wait until you reach Galapagos; the streets are lined with agents selling tours. This is ideal if you don’t mind which tour you do. We knew we wanted to visit certain islands and we wanted the tours booked before we left home.

There are a great many tour operators and travel agents selling day tours but they are all selling the same trips. There are a limited number of boats. Not every island can be visited by every boat as landing licences are limited. Also not all tours run every day. So do make sure you plan accordingly.

Some boats are better than others which is reflected in the price. We opted for a higher standard of boat and loved our choices. What you choose will be down to budget but if you can afford it then don’t skimp. All of our tours included hotel pick-up and breakfast, lunch and snacks and drinks onboard. And all tours are accompanied by a qualified expert Galapagos botanist or geologist as well as a large crew.

In the end we absolutely loved our day trips. They were the highlight of our Galapagos visit. If we could have stayed longer then we would have paid to do more tours. We have zero regrets on our choices.

Day tours when island hopping are not cheap 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 every penny. We did visit some of the more distant islands, we loved the journeys to the islands and learned so much from the guides.

Top Tip : Do lots of research on the different islands and tours. 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 walk around the islands so this was important for us; others may not wish to hike so you’d choose differently.

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

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 online, including the island-hop flight with Emtebe. We booked our accommodation through and researched day tours using Viator and TripAdvisor. The tours are excellent and there are plenty of free activities on each of the main islands.

Island hopping in the Galapagos is a great way to see each island at your own pace. Our only regret was not allowing more time on each island.

Don’t Forget Travel Insurance

Whenever you travel, you should have a great travel and medical insurance policy.  None of us expect anything bad to happen, but in the event of an incident, you want to be sure that your insurance will be there for you.

I’ve ended up in hospital in Peru, Indonesia, Portugal, Japan and Ireland! Every time my insurance took care of everything. I would never leave home without full and comprehensive insurance.

TrueTraveller : We have this policy and we are very happy with the cover, especially considering our ages and pre-existing conditions.

Globelink : We have used and recommended Globelink for years and we’ve not heard of any issues. They are a great choice for European and UK Residents.

Safety Wing : Many of my travelling buddies from the USA have recommended this company to me, although we’ve not used them personally.

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Colleen in Salamanca on the Via de la Plata

Hey I’m Colleen. I’m married to Gerry, we’ve three fabulous kids and been living in France for almost two decades. I fell in love with Spain in the 1980s and I’ve walked 1000s of miles along the Camino de Santiago. Now we’re exploring and walking the world and I can’t wait to share what we’ve learned!

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