A really good selection of seaside, fine boutique or simple but with character hotels, in Crete is available in Evergreen's rental site. Hotel price more or less determines the standard of the accommodation and reflects other important aspects such as the distance from the sea, the airport or port or the town center.
Usually you will get rooms for a lower rate, if your stay is for more than a few nights, especially in Low and Middle seasons. The Majority of hotels and tourist- properties in Crete are on the North coast of the island. Most of them are in co-operation with tour operators and can only booked through them. But still there are plenty of accommodation in Crete available for independent travelers especially in South coast.