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Macrophytes have recovered in rivers across the world, but long-term data and studies are lacking regarding community assembly and diversity changes coincident with macrophyte recovery. We investigated patterns of aquatic vegetation species composition and diversity in thousands of sites in the Upper Mississippi River, USA, spanning 21 y of monitoring and a period of vegetation recovery. We analyzed site-level compositional dissimilarity and environmental associations using non-metric multidimensional scaling, compared stability of lake-level assemblages over time with convex hulls, and assessed shared trends in assemblage dissimilarity at the pool scale using dynamic factor analysis. Site-level differences in aquatic vegetation assemblage structure were associated with water depth and substrate, and a gradient of species abundance and diversity was apparent. A common trend in assemblage …