As a result of hard coal mining, specific areas of subsidence basins, which are often waterlogged, were created in the Czech part of the Upper Silesian Coal District. These areas may not have a high ecological value or, on the contrary, promising biotopes may arise here under suitable conditions, which should be our goal. As part of this work, the above-ground vegetation, and the soil seed bank (using the cultivation method) were investigated. The concentration of the risk elements chromium and arsenic, which are usually increased in mining areas, was determined by neutron activation analysis. Other environmental variables that can affect both the vegetation and the soil seed bank of subsidence basins (fine earth, slope, biotopes, and their representation in the vicinity) were also determined. Using multivariate DCA analysis, a statistically significant influence of chromium concentration and other variables on above-ground vegetation, characterized by the occurrence of many metallophytes and their high coverage, was found. The soil seed bank, which can impact the further development of vegetation, is mainly influenced by forest and wetland biotopes and the representation of areas covered by tailings in the vicinity of sampling sites. It is evident that there are species capable of resisting or accumulating chromium and arsenic pollution in both the above-ground vegetation and the soil seed bank, which can lead to the gradual rehabilitation of subsidence basins. This research can lead to a better understanding of the development of subsidence basins to increase their future ecological values.