Content and composition of ice inclusions are the important characteristics of the redistribution of substance in river ecosystems, which allows taking into account transport of the inclusions matter during the spring ice drift. The data on the composition of the ice cores from the Middle Amur (Khabarovsk water node) after the extreme flooding in 2013 and its terrigenous, chemogenic (formed through chemical processes) and biogenic (diatoms) components are presented in this paper. The importance of the work lies in the fact that the impact on the river ecosystems of catastrophic floods, such as the 2013 flood on the Amur River, due to their uniqueness, has been extremely poorly studied. The analysis showed that the content of terrigenous material and its variation in ice thickness does not exceed the average multi-annual values. The particle-size distribution of the terrigenous material (on their volume and the number) corresponds to that of the river suspended matter, warps (silt deposits on the flood plain) and bottom sediments in the studied river area. Composition of diagnosed chemical inclusions (neoformations of calcite CaCO3 and pyrite FeS2), their number and size depends on the chemical composition of water during the freeze-up and redox conditions in the layer. Flooding had the main impact on biogenic inclusions (diatoms). The change of the leading species (from single population Aulacoseira islandica to Stephanodiscus hantzschii Coscinodiscophyceae class, Stephanodiscaceae family, genus Stephanodiscus) was fixed. This is one of the main indicators of structural and functional violations orderliness hydrobionts. The change in the composition of the leading species associated with the arrival of eutrophying substances and pollutants from the Sungari River (the largest tributary of Amur River) as a result of outcome flooding agricultural lands and residential territories.