The booking sites, like Hotels.com or Booking.com only have access to a portion of the available rooms. In other words, if a lodging (hotel, casa rural, listed alburgue, etc) has 100 beds available, the reservation sites might only have access to 30 beds. That means that 70 beds are available for same day check in, or can be accessed only through the lodging itself.
I ran into this for a reservation I wanted at Hostal Suso for October this year, which is in Santiago de Compostela. Hotels.com, Expedia, Travelocity, Booking.com all showed no availability. So I emailed the property requesting a reservation, and I now have the room I wanted reserved.
So, if you know what date you need a room, and you can't make a reservation from those Booking.com-type sites, you can contact the property directly through their website, email, or by phone and likely secure a reservation.