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Freshwater marshes are the only significant natural ecosystems remaining in the Buenos Aires province section of the Lower Delta of the Parana River (Argentina), occupying 80% of the total island area. The Lower Delta hydrology is dominated mainly by the Parana river and the De La Plata estuary; different temporal superpositions of floods and landscape configurations of the islands result in four distinct flooding patterns. We studied the response of freshwater marsh vegetation to the flooding patterns using principal component analysis and cluster analysis. The study area was gridded and 13 cells were selected representing the different flooding patterns. We found significant environmental heterogeneity in the region and a consequent response in the vegetation, expressed through successive species replacements, and variation in species richness and the number and type of dominant species. The environmental heterogeneity of the region is caused by hydrological variations, geomorphological changes in the islands from upstream to downstream areas of the delta, and patterns of human activity.