Our study provides insights into the spatio-temporal dynamics of macrophyte assemblages in the Danube Inland Delta, situated in the northwest part of the Pannonian lowland on the Slovak-Hungarian border. A total of 63 aquatic plant species were recorded at six monitored sites during the years 2003-2020, including 1 endangered, 2 vulnerable, and 1 neophyte species. Macrophyte data from long-term monitoring were used to test the hypothesis that aquatic plant assemblages in the hydrologically disturbed Danube riverscape have become more taxonomically and functionally similar over the past 17 years. Although a decline in the taxonomic and functional richness of macrophyte assemblages was observed at most monitoring sites, no evident year-to-year decrease in their heterogeneity was noted for either aspect of biodiversity. However, a significant decline in taxonomic and functional richness, as well as in the heterogeneity of the macrophyte community across the entire monitored area, was observed during the study period. While a decrease in species number represented approximately one species per year, the taxonomical beta diversity, including its taxonomical turnover component, also declined, with a mean annual decrease of 0.5% and 0.7%, respectively. Using abundance class data, the mean annual decrease in beta diversity was 0.6%. A time-series analysis of macrophyte functional traits (growth form, dispersal unit, and strategy) revealed that aquatic plant assemblages from different monitoring sites converged toward a narrower range of functional structure. The mean annual decline in macrophyte functional heterogeneity was 0.7% based on abundance class data and approximately 0.3% based on incidence data.