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Travel in Iraklion, Crete

I have only day to travel on Crete. We are flying from Athens and want to see the Knossos Palace and the Archaeological museum and the town around the Archaeological museum. I have tried figuring out the bus schedule! I can't determine if you can travel directly from the airport to Knossos or if you can only travel from the port to Knossos. I also can't make heads or tails of the schedule, even in English. I know hiring a taxi would be simpler, but I am also considering budget. Any ideas?

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There does not appear to be a bus from the airport to Knossos. You will have to get to the bus station near the ferry port where there are regular buses to Knossos. Even though you are on a budget it would probably make sense to take a taxi to Knossos then the bus to the port bus station. From there is is an easy walk to Central Heraklion and the museum. Easy bus ride back to the airport as well. Depending on when your flight arrives you may want to take the bus to Heraklon, visit the sites there and take the bus to Knossos in the late afternoon. It gets very hot out there around 10 to 3. This way you won't need a taxi at all.
City Buses (blue) serving the city of Heraklion from early morning until late evening. Starting from the port city services operated in the archaeological site of Knossos. Information: 2810-226065 and 220795. Web: http://astiko-irakleiou.gr/
Here are images of Central Heraklion. Its worth a few hours to just wander the old town and Venetian harbour and of course the newly reopened Castello.
Heraklion https://www.flickr.com/photos/stanbr54/sets/72157655935354556