Floodplain rivers constitute a network of environments with different connectivity degrees and capability to exchange organisms and matter. The Paraná River is one of the tenth largest floodplain rivers of the world, and its configuration and dynamic resembles that proposed by metacommunity approaches. With this frame, we study the eukaryotic microorganisms’ diversity at the main channel and floodplain environments of the Paraná River (Argentina) in order to understand the community assembly rules and the driving factors.