The expanding demand for new critical raw materials can lead to their increased release to the environment in the form of emerging environmental contaminants (EECs). However, there has never been a comprehensive study that takes into account the total EEC content, the content of various EEC fractions, their behaviour in floodplain soils, and potential ecological and human health risks. The occurrence, fractions, and influencing factors of the seven EECs (Li, Be, Sr, Ba, V, B, Se) originating from historical mining in floodplain soils of various ecosystems (arable lands, grasslands, riparian zones, contaminated sites) were investigated. Based on the evaluation of the overall levels of EECs (potentially toxic elements) in comparison to the soil guideline values set by European legislation for Be, Ba, V, B, and Se, it was found that only Be did not exceed the recommended limits. Among the elements analyzed, Li had the highest average contamination factor (CF) of 5.8, followed by Ba with 1.5 and B with 1.4. Particularly concerning was the discovery of a potential serious health risk associated with Li exposure for children, as indicated by hazard quotients ranging from 0.128 to 1.478. With the exception of Be and Se, the partitioning of the EECs into the different fractions revealed that the EECs are primarily bound with the residual fraction. Be (13.8%) had the highest percentage of exchangeable fraction as the most bioavailable in the first soil layer, followed by Sr (10.9%), Se (10.2%), Ba (10.0%), and B (2.9%). The most frequently observed correlations were between EEC fractions and pH/KCl, followed by soil organic carbon and manganese hydrous oxides. Variance analyses confirmed the impact of different ecosystems on EEC total content and fractions.