Day trip to Akrotiri in Santorini from Chania

Direct Ferries does not show a ferry from Chania to Santorini but it does from Heraklion to Santorini on SeaJets. The ferry departs Heraklion at 8a arriving at Santorini at 9:50a. A taxi will cost $100 to get to Akrotiri’s archeological site but you can take a shuttle for half the price that will drop you off at the museum.
You’ll need to take a taxi back to the port with a ferry departing at 3:50p. No need to book ahead because there will be lots of seats, these vessels are big. When you hear Santorini is the next stop go down stairs and stand where you need to be before the boat stops. Stops are brief and as soon as you get off, it pulls away.

I will be doing a Crete to Santorini in June and found a direct ferry from Rethymno to Santorini. Not sure if they run these every day.

The Seajets Rethymno ↔ Santorini ferry only operates on Tuesdays and Saturdays and only from Saturday 27 May.
There are no ferry line between Chania and Santorini, you will have to go to Heraklion to catch a ferry.
If you have a car, to catch the first ferry to Santorini you will need to leave Chania at 5am max.

Here are the schedules Heraklio →Santorini in two weeks:

http://www.openseas.gr/HER/JTR/2023-05-18/2023-05-18/itineraries

And the Santorini → Heraklio return schedules:

http://www.openseas.gr/JTR/HER/2023-05-18/2023-05-18/itineraries

The fastest return ferry trip will cost you around €190 per person.

The round trip by taxi from the port to Akrotiri will in my opinion certainly cost you more than 100€.

There is no direct bus from the port to Akrotiri, you have to take a bus to Fira and then one from Fira to Akrotiri.
In the best case scenario by bus you will not be in Akrotiri until 11:00 am.
Between Fira and Akrotiri there is a bus every 30 minutes. Same for the return

The total cost port-Fira-Akrotiri round trip by bus will be 7.20€

To take a ferry back to Heraklion you will have to be at the port by 5:00 p.m. max, so leave Akrotiri at 3:30 p.m.
max if you take the bus or 4:30pm max if you are lucky enough to get a taxi.

Still with luck and a rental car, you'll be back in Chania around 10 p.m.

Be careful, if for some reason you miss your return ferry you will be stuck in Santorini until the next day.

Crete has the most archeological sites of any island and you'll find them all over the island.

There's more than enough to keep you occupied on Crete rather than spending a huge amount of money to go and return from Santorini plus the time involved for just a day trip.

Thank you all; this is very helpful. I’ll rethink my usual tendency toward scope creep.

The only reason we returned to Santorini was to visit Akrotiri as it had been closed on an earlier trip due to a roof collapse that had killed tourists.
We were determined to see it. It is an excellent archeological site but I don’t think it was worth a special trip just to see it, especially since we didn’t like Santorini on our first visit, nor on this second visit either.

Oh my gosh there is so much to see on Crete that it would be a real waste to spend 9 hours in transit for this visit.

Suki and Emily, thank you. Your comments help me feel more settled about saving Akrotiri for next time.