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The best times for visiting Crete is May, when every outcrop of rock is ablaze with brilliant wildflowers and the sea is warm enough for a brisk dip, or September and October, when the sea is still warm and the light golden but piercingly clear. A spring visit comes with the advantage of long days.
Crete is really only noticeably busy from mid-July through August, when the main Minoan sights and towns on the north coast come close to overflowing with tourists. Take special care at these times to avoid such places as Mallia and Limin Hersonissos, hideously overdeveloped towns where bars and pizzerias fill up with heavy-drinking northern Europeans on summertime package tours.
Even in the height of summer, though, you can enjoy many parts of the west coast without feeling too oppressed by crowds. Crete can also be a pleasure in winter, when you can visit the museums and archaeological sites and enjoy the island's delightful towns without the crush of crowds. Remember, though, that rainfall can be heavy in January and February, and note that many hotels and restaurants, especially resorts, close from late October or November through mid-April or May.