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In lowland streams, channelization is a severe hydromorphological modification with negative impacts on ecosystem functioning and biological communities. We assessed the functional structure and spatial patterns of macrophyte assemblages in channelized streams, and we identified the most affected traits by this practice. We studied unchannelized (UCS) and channelized sites (CS) using a null model approach and functional diversity indices. The macrophyte coverage was higher in the UCS (mean: 86 ± 15 %) than in the CS (50 ± 35 %). Unchannelized sites revealed a random pattern, with predominating submerged and free-floating species, as well as reproduction by turions and tubers. Channelized sites showed a segregation pattern (C-score obs.: 23.08; C- core exp.: 22.20; SES: 3.20) of functionally similar species indicating interspecific competition, and lower functional richness, evenness, and Rao quadratic entropy compared to the UCS. The predominant traits found for macrophyte assemblages of these sites were emergent life form, and dispersion by stolons. Our results indicate that in CS, the abiotic environment and biotic interactions act as filters and only macrophyte species with key traits can colonize these streams. In this sense, the creation of backwater areas, the reestablishment of longitudinal and lateral connections of the streams, as well as macrophyte transplants could favor the dispersal and establishment of macrophyte species. These rehabilitation measures could positively improve the functionality of these ecosystems.