We are staying a few days in Milan and want to venture to Lake Como and visit Bellagio, Varenna etc...Rather than book an all day scripted tour, we would rather do our own itinerary for the day. Is there good transportation from Milan to Lake Como? Easy to leave from there to other destinations?
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Enjoy this beautiful area and safe travels!
There is an hourly train from Milano Centrale to Varenna. A short walk to the ferry dock for ride to Bellagio and Menaggio.
You will want to return. As you walk around Bellagio, go to the upper part, visit historic church, see views and consider where you might want to stay in the future such as Hotel Belvedere.
Day tripping from Milan to Lake Como is what I did and highly recommend it. Get on a direct train (no transfers) at Milano Centrale to Varenna-Esino (1h 15m). Tour Varenna that sits on the lake before jumping on the 15m ferry ride to Bellagio and explore there. The mountains add a very dramatic backdrop making this probably the most scenic spots on the lake.
And once you're done with Bellagio, if the boat schedule works out, instead of backtracking to Varenna you can take the ferry to Como town and take the train from Como Nord station back to Milan (I think those trains go to Cadorna station, but you can change trains in Saronno if you need to go to Centrale).
That way, your day trip becomes a loop.