Rice fields are an important habitat for waterbirds. Knowledge of the availability of this habitat is important since the reduction in the area of natural wetlands has converted rice fields into vital refuges. This paper presents a method for mapping habitat availability in rice fields according to different waterbirds’ habitat preferences and examining its phenology during the crop cycle. Data from bird censuses carried out in the Doñana rice fields were analysed to determine the habitat preferences of 22 species of waterbird at different stages in the rice production cycle. Discriminant function analysis of seven Landsat images was used to classify paddy field stages. The phenology of habitat availability in rice fields during autumn and winter was examined. Waterfowl and waders preferentially used the ‘flooded’ and ‘mudflats with water’ paddy field stages, respectively, and the ‘rice growing’ and ‘dry’ stages were rejected by waterbirds. The area of preferred habitats within rice fields increased during autumn; subsequently, the area of the ‘flooded’ paddy fields decreased in January, whereas that of ‘mudflats with water’ remained available until March. The automatic classification of paddy field stages with Landsat images allowed habitat availability for different species of waterbirds to be monitored and provides relevant information for understanding behavioural and population responses in waterbirds that use rice fields. After examining the phenology of the availability of habitat and comparing it with dates of arrival and departure of migrant waterbirds, best crop practices could be defined to favour waterbirds (i.e. adjusting harvest, ploughing and flooding dates). Taking into account climatic change and loss of wetlands this method could help in the integration of agriculture and conservation, in particular in areas where there is no remaining natural wetland habitat.