Natural floodplains are rapidly disappearing ecosystems worldwide, primarily due to changing hydrology. Continental Croatia harbours some of the largest remaining and best preserved natural riverine floodplains in Europe. To establish conservation priorities, we surveyed water beetle assemblages in three large floodplains situated in the Danube, Drava, and Sava basins (Ramsar sites Kopacki rit and Lonjsko polje, and Spacva riparian forest), with special focus on the red-listed beetle Graphoderus bilineatus. The main aim of our study was to investigate the key environmental factors driving variation of water beetle assemblage structure and occurrences of G. bilineatus. Environmental variables describing habitat types and various habitat characteristics were measured and/or estimated for each sampling site. A total of 4.339 water beetle specimens belonging to 98 species were recorded. G. bilineatus was recorded at two out of the three investigated floodplains at 14 out of 30 sampling sites. We found significant differences in water beetle assemblages among the three localities based on the total species dataset, accompanied by different environmental background and vegetation composition. The density of riparian vegetation, permanent water durability, shading, type of bank, and plant communities best explained the distribution of the water beetle species. Based on the regression model, human impact and shading have significant effects on the abundance of G. bilineatus. Sites with G. bilineatus presence have significantly higher species richness compared to the sites without the species. Co-existence analysis indicates various types of associations between G. bilineatus and other water beetle species.