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The roots of Eichhornia crassipes provide different microhabitats for invertebrates, including substrate for the Asian invasive bivalve Limnoperna fortunei. This work evaluated the density and size structure of L. fortunei on the roots of E. crassipes in lentic waterbodies associated with the Middle Paraná floodplain. The field work was carried out between November 2009–2010, covering different phases of the hydrological regime. Floating meadows of E. crassipes were sampled monthly in two lakes with different degrees of connection to the main channel of the Paraná River. Bivalve densities were not associated with variations of the biomass of E. crassipes roots and the highest mussel densities were recorded during months of high temperature. The maximum size recorded in both lakes corresponded to individuals approximately 2.5 years old; however, up to 75% of the molluscs were represented by pre-reproductive individuals (up to 6 months old). In these lakes with soft bottom and limited hard substrates, E. crassipes is an important site for the mussel attachment during its early stages of development and could not be the final site of settlement during its lifecycle.