Pension Erofili
Well located hotel run by a helpful and friendly couple, more modest in its appointments than many Hydra hotels but also less expensive; in addition to standard rooms there's a studio with kitchenette.
Ippokampos Hotel
Attractive island atmosphere at this moderate/upper priced hotel makes it one of the better choices in its category. Open May - October.
Botsis Guest House
Guest House 70 meters away from the harbor with a fridge a TV and A/C in every room. Also every room has a private balcony with view something you won't find that often in Hydra due to the strict building code.
There are plenty of small hotels and guest houses in Hydra Island for those who don't want to limit their visit to a day trip. Note that some Hydra accommodations may be accessible only by climbing stairs, so if this is a problem for you, ask when booking.