Despite efforts to quantify the impacts of land cover change on wind erosion, assessment uncertainty remains large. We address this uncertainty by evaluating the application of ecological site concepts and state-and-transition models (STMs) for detecting and quantitatively describing the impacts of land cover change on wind erosion. We apply a dust emission model over a rangeland study area in the northern Chihuahuan Desert, New Mexico, USA, and evaluate spatiotemporal patterns of modelled horizontal sediment mass flux and dust emission in the context of ecological sites and their vegetation states; representing a diversity of land cover types. Our results demonstrate how the impacts of land cover change on dust emission can be quantified, compared across land cover classes, and interpreted in the context of an ecological model that encapsulates land management intensity and change. Results also reveal the importance of established weaknesses in the dust model soil characterisation and drag partition scheme, which appeared generally insensitive to the impacts of land cover change. New models that address these weaknesses, coupled with ecological site concepts and field measurements across land cover types, could significantly reduce assessment uncertainties and provide opportunities for identifying land management options.