The Upper Paraná River floodplain is one of the few remaining non-dammed stretches in Brazil. It has a typical fluvial dynamics represented by the flood pulse and a highly complex habitat, which allows the existence and maintenance of a great biodiversity, including diatom species. As it happens in tropical lowland environments, also in this floodplain, the genus Eunotia is one of the most diverse and abundant diatom groups. Therefore, this study addresses morphologic and morphometric details of a new species and the most abundant Eunotia species in sediment cores from two wetland lakes. The morphological characteristics from each species were obtained through microscopy documentation of cell walls, and compared with other related species.