Extensive soil sampling and screening assessment of ecosystem risks combined with a multidimensional statistical analysis were used to estimate and spatially characterize the ecosystem risks stemming from the contamination of floodplain soils in the Czech Republic. We proved structural differences in regional pollution patterns where different regional/local pollution sources led to various nature and extent of the environmental load of floodplain soils. The established spatial patterns helped reveal the areas where soils do not meet soil quality standards and where the ecosystem risks were elevated. Furthermore, the results allowed to establish priority contaminants of flood affected areas in various catchments in the Czech Republic. Combining both the magnitudes of estimated ecosystem risks and structural characteristics of pollution profiles, the highest estimated risks showed the localities with high contents of organochlorine pesticides, several samples connected to geochemical anomalies of metallogenic zones (deposits), and localities with a long history of industrial load. Since extreme weather events have recently become more frequent, our results highlight the importance of a continual monitoring of pollutant turnover in floodplain soils with a high flood frequency.