The ventilation duct system (1,24,34) comprises waste receiving means (2) configured for receiving waste (17,20,32) from at last one animal habitat surface (3) of an animal habitat structure (25,33,52) and is located at least partly below the animal habitat surface (3). It comprises means for generating a pressure difference between a first long side (10) and an opposing second long side (11) of the waste receiving means (2) to generate an air pressure gradient across the width of the waste receiving means (2). It further comprises regulating means (35,36,38,39) for regulating natural ventilation located away from the waste receiving means (2) and adapted to control airflow in the animal habitat structure (25,33,52). In the method, the combined operation of regulating means and the air pressure gradient across the width of the waste receiving means is used for providing improved ventilation of the animal habitat structure.
