The intensification of crop management in the U.K. over the past 60 years has resulted in the decline of the populations of a number of annual plant species adapted to arable habitats. In contrast, other species continue to be common as arable weeds. A community assembly approach was taken to explain these recent changes in the weed flora using databases of plant functional traits, a pot experiment, and weed surveys of the Broadbalk long-term experiment. The hypothesis was tested that species that have been selected against by increased fertilizer inputs and herbicide use share an adverse combination of traits. An analysis comparing the combination of maximum height, seed weight, and time of first flowering of 29 common and 32 rare or threatened U.K. autumn weeds established that rare or threatened species occupied an area of trait space that was distinct from the common species. A rare weed trait syndrome of short stature, large seed, and late flowering was identified. The theory that species with a trait syndrome that is currently unfavorable are better adapted for less fertile environments was supported by the pot experiment. Species with a combination of short stature and large seed had a relatively greater competitive ability in low compared to high fertility treatments. Analysis of survey data from the Broadbalk long-term experiment confirmed that, as N inputs increased, the abundance of the two functional groups that contained only common species remained stable or increased; whereas, the groups dominated by rare or threatened species declined as fertility increased. An understanding of the response traits of arable plants to management filters, including fertilizer inputs and herbicide, is valuable for designing conservation strategies for rare species or predicting future shifts in the functional diversity of weed communities including the potential for invasive species to establish.