Neotropical aquatic ecosystems have a rich aquatic flora. In this report, we have listed the aquatic flora of various habitats of the upper Paraná River floodplain by compiling data from literature and records of our own continuous collections conducted during the period 2007-2009. Our main purposes were to assess the macrophyte richness in the Paraná floodplain, to compare it with other South American wetlands and to assess whether the number of species recorded in South American inventories has already reached an asymptote. We recorded a total of 153 species of macrophytes in the Upper Paraná River floodplain, belonging to 100 genera and 47 families. In our comparative analysis, a clear floristic split from other South American wetlands was shown, except for the Pantanal, which is the closest wetland to the Paraná floodplain and, therefore, could be considered a floristic extension of the Pantanal. The species accumulation curve provides evidence that sampling efforts should be reinforced in order to compile a macrophyte flora census for South America. The high dissimilarity among South American wetlands, together with the lack of an asymptote in our species accumulation curve, indicates that the sampling effort needs to be increased to account for the actual species richness of macrophytes in this region.