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Agricultural intensification in Europe during the past 30 years has led to changes in compositional and functional weed structure in agroecosystems as well as increases in the prominence of alien weeds. Irrigation is a major driver of agricultural intensification, particularly in semi-arid zones of the Mediterranean. In the past few decades, irrigated land has expanded in semi-arid agricultural lands in northeastern Spain. The goals of this study were to identify long-term temporal changes in compositional and functional weed communities in annual (i.e. maize crops) and perennial (i.e. orchards) irrigated crops of this area and determine whether these changes differentially affect native and alien plants. Changes in the diversity, composition and functional groups of the weed communities in fruit-tree orchards and maize crops were assessed using plant surveys in 1989 and 2009. During the studied period, a decrease was recorded in the diversity of native species in the fruit-tree orchards; this decrease was accompanied by an increase in alien weed diversity and a general homogenisation of species in the weed community. In the maize crops, the diversity values of native and alien plants changed little during 20 years. The identification of functional groups revealed that most of the species whose cover increased in the fruit-tree orchards were graminoid alien species that perform C4 photosynthesis and disperse seed via water or a combination of vectors. In the maize crops, the identified functional groups did not differ in the proportion of species whose cover changed between 1989 and 2009. Hence, in irrigated orchards the observed changes in the weed community and the prominence of alien species are mediated by the selection of a set of traits that let species to overcome management filters. Similarly, the stability of functional composition of weed communities in maize fields is the result of the selection of species functionally similar to the crop.