Crete - some help fine tuning my vacation needed!

For Balos, the easiest way will be to drive to Kissamos paort (after Kissamos town) to get the boat trip, you can book online, depending on the season there are either 1 or 2 companies doing the trip.

from Chania for Samaria gorge you can either buy a ticket with a tour agency (you can get it the day you arrive in Chania, Halidon St & around there are many small tourist offices, all offer the same trip). Or you can just go on the public bus & ferry from the central bus station. I assume you are aware it is an 18km, long, hot, difficult hike, with the 1st 2 km down uneven wooden stairs & the rest on stony rough paths? You need good walking boots & most people like to schedule a quiet day the following day.

Elafonisi is just under 2 hours drive from Chania. It is nice to drive through Topolia gorge (you can stop to see the cave church of Agia Sofia) & back around the coast. Or go via some of the traditional villages, like Elos & Kandanos, particularly important if you have any interest in WWII. Or detour to the eco-village of Milia, only if you like long drives on tiny dirt roads! an amazing place. At Elafonisi, Do walk across to the 'island', you may need to wade through the little channel, as that is where the beach is prettiest & pinkest. I recommend going early in the day as the beach gets full by midday.

Don't forget to give yourselves a minimum of 1 day in Chania itself, a wonderful ancient city, stroll around the Venetian harbour & many tiny alleyways etc.

You could stop off at Aptera & Rethymno on your way to Heraklion, that is probably plenty for 1 day. Seitan Limani is the opposite direction & not easy to access. Or go to Heraklion earlier to see the modern Archaeological museum.

Not quite what you asked, but perhaps a different suggestion. Ditch the car and take the bus to the entrance to the Samaria gorge. At the end, stay the night in Agia Roumeli. The next day, take the ferry to Palaiochora and stay the night there. It's a nice little town. You could do Elafonisi beach the same day, there will be time.

The next day, head back to Chania and slowly make your way to Heraklion, stopping and checking out various towns along the way.

Yes, you'll miss Balos beach, but you will have spent the day at Elafonisi which I think is nicer. You'll see more this way and you hit everything on your list, minus Balos.

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