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 dissimilarity over time and across contiguous floodplain lakes indicate that assemblage composition changed and diversity increased with considerable synchrony within the past 21 y. Shared trends across the 400-km study reach are indicative of 1 or more widespread, common drivers; however, neither hydrologic extremes nor turbidity explained vegetation assemblage patterns. Following several years of strong changes in composition and increased diversity, the vegetation assemblage displayed signs of increasing stability in some pools but not others. Further research is needed to identify drivers and mechanisms of aquatic vegetation assemblage expansion, assembly, and resilience, all of which will be applicable to the recovery of aquatic vegetation in floodplain systems worldwide.