Considering the effects of rapid population growth, urbanisation and climate change in recent years, the protection of freshwater resources, the prevention of water pollution and the proper sharing of freshwater resources among different sectors have become important issues. Water footprint (WF) is a sign of freshwater use and is not only an indicator that can be used in the climate crisis, but also to protect water against nitrate pollution. In this study, the Küçük Menderes Basin was chosen as the study area due to different crop varieties. Agricultural crop patterns were classified using Rapideye and Sentinel-2 satellite images of the study area obtained in 2017. Thus, the cultivated areas were obtained for cotton and maize (grain and silage) in the basin. In particular, agricultural crop patterns were considered in which agricultural production was intensive and blue water was used predominantly. As a result, the first-crop corn production, which has a high blue WF of 3840 m³/ton in the basin, has the highest greywater footprint due to the use of intensive chemical fertilisers. This was followed by cotton with 2331 m³/ton, and the second-crop silage corn production had the lowest greywater footprint. Agriculture’s water footprint assessment provides a solid foundation for planning climate change adaptive crop production, managing nitrate-sensitive areas and anticipating future regional changes.