The study evaluated the influence of aquatic environmental features, morphological and functional traits of water bodies and directional spatial processes on the macrophyte community of floodplain ecosystems formed as a result of water flow regulation by the construction of dams. The fluvial processes were found to be still the main factor in the formation of geomorphological and ecological characteristics of floodplain ecosystems, and also determine the spatial patterns of variability of aquatic macrophyte communities. The influence of water properties on macrophytes is significantly spatially structured, as it is modified by the morphological and functional characteristics of the water bodies. The exchange of water in the floodplain system is influenced by the functional types of water bodies, which explains their significant correlation with spatial variables. The development of macrophyte communities on a broad scale is driven by the characteristics of the aquatic environment, the morphology of the water bodies and the functional types of the water bodies. On a fine scale, the patterns are described by a pure spatial component. The impact of fine scale patterns on the variability of macrophyte communities increases with increasing community disturbance, both natural and anthropogenic.