Several large rivers worldwide have recently undergone noticeable improvements to water quality, a process called re-oligotrophication. Here, we leverage a massive macrophyte and water quality dataset covering two decades of long-term biomonitoring that reveal change within a ~400 km stretch of the Upper Mississippi River, U.S.A., which experienced major changes to hydrology and water quality, as well as experienced minor changes to climate during the study from 1998–2020. We employ a joint species distribution model to understand how progressive re-oligotrophication and changes in the hydrological conditions affect macrophyte taxonomic and functional diversity at a macrosystem scale. We uncovered substantial macrophyte community recovery during recent decades evidenced by increased species prevalence, taxonomic and functional diversity, as well as a community shift away from previously dominant, undesirable free-floating plants towards more desirable submersed plants. More than half the species responded positively to re-oligotrophication (specifically, reduced concentrations of total phosphorus, chlorophyll a, and total suspended solids). However, total nitrogen concentrations continually increased over the 22-year period that negatively affected the occurrences of nearly all species. The macrophyte traits of pollination mode and life form explained a large proportion of the environmental responses at the metacommunity-level. Lastly, species associations were strongly affected by the spatiotemporal scale at which these were viewed. Our results show that riverine macrophyte occurrence and community diversity were greater after re-oligotrophication and with increased discharge that created more suitable aquatic habitat. Although re-oligotrophy partially explained macrophyte recovery, the spatial heterogeneity of the riverscape was also important for structuring the recovering macrophyte community.