The floodplains of large European rivers are today the most threatened water ecosystems, since the floodplain river valleys have been systematically drained over the past century. One of the largest preserved natural floodplains of the Danube is the Kopački rit. The goals of this study are as follows: i) to create a complete list of phytoplankton biodiversity of the Lake Sakadaš, the deepest depression in the floodplain Kopački rit, observed over a period of half a century; ii) to report frequency of the most important taxa with emphasise on the blooming species and particularly on invasive alien and toxic species; iii) to indicate on the possible impact of global changes on phytoplankton biodiversity in the investigated floodplain lake. A great diversity of phytoplankton, hundreds of species can be expected. A high phytoplankton diversity registered in the investigated floodplain lake can be explained by considering both local (i.e. environmental filters) and regional (i.e. dispersal) processes as responsible for structuring microbial communities. The crucial role in the maintaining high biodiversity have hydrological connection between various types of biotopes which are existed on a large natural area of the river-floodplain system. Therefore, preserving the dynamics of flooding is the basis for protecting the biodiversity of this and similar river-floodplain systems.