How to Get from Isabela to Santa Cruz: Why We Took the Ferry

There are two options to get from Isabela to Santa Cruz: fly or ferry.

Unlike the San Cristobal to Isabela route we did where flying is the obvious choice (no direct ferry exists between those two islands), this route has a genuine decision to make.

Why we chose the ferry

Two ferry departures are available: 6 am and 3 pm. We chose the 6 am for two reasons: seas tend to be calmer in the morning, and it is cooler.

There are several ferry boats operating this route, but the Queen Arlett appears to be the newest and largest of the options we saw at the pier that morning. That made us happy with our choice.

Here is why the ferry made more sense than flying for us:

The flight does not land where you think it does.

Here is something worth knowing before you book the flight: Emetebe does not land in Puerto Ayora.

It lands on Baltra, a completely separate island. From there you are looking at a bus, a water taxi across the Itabaca Channel, and a 40-minute taxi ride before you see your hotel.

The flight departs at 9 am and touches down around 9:30 am. Factor in all those transfers and 9:30 am quickly becomes 11 am.

The ferry drops you right where you need to be.

The Queen Arlett arrives at the Puerto Ayora pier around 8 am. Our hotel, El Barranco, was a five-minute walk from the dock.

We stepped off the boat, rolled our bags down the waterfront, and were checking in before people on the Emetebe flight had even left Isabela. By 9 am we were getting settled with a full day on Santa Cruz ahead of us.

Two full hours earlier than flying, with a fraction of the logistics.

El Barranco full review coming soon. Short version: book it.

The cost comparison:

• Queen Arlett ferry: $35 per person
• Emetebe flight (Isabela to Baltra): $157 to $192 per person depending on the fare selected + $5 bus + $1 water taxi + $30 land taxi 

One more factor: timing and conditions. We traveled in mid-May, a transition month with generally calm seas.

Alicia from Agora Tours, who arranged our booking and who I trust completely after using her for multiple tours on this trip, confirmed that May conditions are usually still good for ferry travel.

Had we been traveling later in the year when seas get rougher, we would have flown without hesitation.

For the full ferry vs flight breakdown by season and route, read my Ferry or Flight Between Galapagos Islands guide.

We booked through Agora Tours about 6 weeks in advance.

Alicia, who co-owns Agora Tours with her husband Carlos, is responsive via WhatsApp and follows through on bookings.

She also handled our Los Tuneles tour and Las Tintoreras tour on Isabela, so by the time we booked the ferry we already trusted her completely.

I did try reaching out directly to the ferry operator before booking. The communication was not the best. That experience alone was enough to confirm that booking through Alicia was the right call.

One less thing to chase down on a busy trip.

Wake up: 4:30 am

Yes, really. The ferry departs at 6:00 am and you need to arrive at the pier at 5:00 am.

We pre-arranged a $5 taxi from our hotel the night before. We were at the pier by 5:05 am.

One unexpected highlight of the whole early morning chaos: the sunrise over the water as we crossed to the Queen Arlett on the water taxi.

All that 4:30 am alarm pain, all the pier logistics, and then you are sitting on a water taxi in the pre-dawn quiet watching the sky turn orange and pink over the Galapagos. Wow.

The 2 Piers

Worth knowing before you arrive: there are actually two piers on Isabela Island.

The smaller pier is where the day tour boats depart: Los Tuneles and Los Tintoreras. That is the pier where you dodge around sea lions just to reach your boat.

They are absolutely everywhere and completely unbothered by the fact that you are trying to board a vessel. 

The main pier, where the Queen Arlett departs, is a different story. No sea lions, more orderly, and exactly where you want to be at 5 am with luggage in tow.

At the Pier … a little confusing at first

Here is something worth knowing before you arrive. When you first walk up to the ferry area, there are multiple representatives standing around for different boats. It is not immediately obvious who is who.

I approached the first person I saw. The ferry name he represented was one I did not recognize. I moved on. The second person represented Queen Jenny, another reputable ferry on this route.

Our Queen Arlett representative arrived a little later than the others.

Do not panic if your person is not there immediately. Just wait near the pier area and they will show up. Have your booking confirmation handy so you can confirm your boat name quickly when they arrive.

The check-in process

Once the Queen Arlett representative arrived, the process moved quickly.

They gave us a lanyard with our boat name. A separate person then collected $1 per person for the water taxi and handed us a laminated ticket.

Three lines formed by boat name and everyone jockeyed for position.

The rain detail

One thing I did not anticipate: a brief downpour while we were standing on the pier waiting to board the water taxi. No rain was forecasted that morning.

The pier is covered, but the wind was strong enough to whip the rain sideways, catching everyone on the periphery. We all shuffled quickly toward the center to stay dry.

The people who were already in the process of boarding the water taxi when it hit got completely soaked.

Not a big deal in the grand scheme of things, but I was wearing city tennis shoes instead of my Teva water sandals and immediately regretted it. Wear shoes you would not mind getting wet.

The Queen Arlett is relatively new, launched in summer 2025, and it shows. It was noticeably newer and larger than the other ferries at the pier that morning.

The Queen Arlett runs one specific route:

• Isabela to Santa Cruz: 6 am departure
• Santa Cruz to Isabela: 3 pm departure

Key specs:

• All forward-facing seats in a 2×2 configuration, like a small aircraft
• Capacity: approximately 50 passengers including upper deck
• 4 engines
• Starlink internet on board (does not always work perfectly but impressive for the middle of the Pacific Ocean!)
• 5 fans and 4 openable windows
• Life jackets and barf bags provided
• Staff: nice, courteous, and safety-conscious

The forward-facing seats are worth noting specifically. Some ferries have side-facing banquette seating where passengers face each other.

For anyone prone to motion sickness, forward-facing seats on a nearly 2-hour crossing make a real difference.

One practical note: There is a second row from the back designated for passengers who are handicapped, pregnant, or traveling with young children (in case that applies to you). 

My husband is prone to seasickness, which was one of our main considerations when deciding whether to ferry or fly. He came prepared with a three-pronged approach:

✔️  An EmeTerm Seasickness Band (the kind that sends mild pulses to the median nerve on your wrist, see photo below)

✔️  Bonine taken 1 hour before boarding

✔️  Ginger chews throughout the crossing

He did great.

Mid-May seas were relatively calm. The crossing had some gentle movement but nothing dramatic.

By 7:45 am it was getting warm inside the cabin, which is another reason the morning ferry beats the 3 pm departure hands down. I cannot imagine doing that crossing in the afternoon heat.

One more thing: Although Queen Arlett did provide a barf bag. I always carry a small trash bag in my bookbag. Just in case. You will thank yourself or you will never need it. Either outcome is fine.

Departed right at 6:00 am.

The Queen Arlett has two levels but no passengers were placed upstairs on our crossing. Everyone stayed on the lower deck. The spray from the water was significant enough that two of the four windows had to be closed.

The forward-facing 2×2 seats gave the whole cabin an orderly, comfortable feel. Nothing like the chaotic side-bench ferries you sometimes encounter on island routes elsewhere in the world.

We arrived at Puerto Ayora at 8:05 AM.

Total crossing time: just over two hours.

Ferries never dock directly at the pier in Puerto Ayora. You always take a water taxi from the ferry boat to the dock on both ends of the journey.

Here is how the luggage works: on the Isabela side, you bring your own suitcase to the water taxi and the crew loads it.

On arrival in Puerto Ayora: the staff unloads your bags and places them on the dock for you to retrieve. Keep your backpack with you at all times throughout.

From the dock, our hotel El Barranco was a 5-minute walk. We had dropped our bags and were out exploring by 9 am with an almost full day on Santa Cruz ahead of us.

That is the magic of the morning ferry.

✔️  Book through Alicia with Agora Tours via WhatsApp, she is amazing to work with!

✔️  Arrive at the pier by 5 am.

✔️  If your ferry representative is not there immediately, wait. They will arrive.

✔️  Bring $1 bills for the water taxi to make it easy.

✔️  Load the water taxi at the exit end to board the ferry first.

✔️  Sit toward the back of the ferry for better airflow if you are prone to nausea.

✔️  Bring seasickness medication, a seasickness band, and ginger chews if you are prone to motion sickness.

✔️  Pack a small trash bag in your backpack. Just in case.

✔️  Keep your backpack with you at all times. Luggage goes separately.

✔️  Morning ferry only. The afternoon 3 pm departure in the Galapagos heat is not appealing.

✔️  Take Bonine 1 hour before you board, not after the nausea starts.

The Queen Arlett ferry from Isabela to Santa Cruz was one of the smoother logistical moments of our entire 17-day trip.

A 4:30 am alarm is a small price to pay for arriving in Puerto Ayora at 8:05 am with a full day ahead of you, a $35 ferry ticket, and zero Baltra airport transfers to deal with.

The morning chaos at the pier is real but manageable once you know what to expect.

Your ferry representative will show up, the process will click into place, and two hours later you will be watching your luggage get lifted from the water taxi onto a dock in one of the most beautiful places on earth.

Worth every early alarm.

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Questions about our ferry experience from Isabela to Santa Cruz with Queen Arlett? 

Let me know in the comments below!