Metal-contaminated mining soils pose serious environmental and health risks if not properly managed, especially in mountainous areas, which are more susceptible to perturbation. Currently, climate change is leading to more frequent and intense rain events, which cause flooding episodes, thereby altering soil redox equilibria and contaminants stability. We evaluated the potential release of Zn and Cd (two of the most common inorganic contaminants) and the factors regulating their solubility and speciation in two heavily contaminated soils representative of a Zn-mining area. The soils were flooded under aerobic (for 24 h) and anaerobic (for 62 days) conditions using mesocosm experiments, sequential extractions, and geochemical modelling. Leaching trials under aerobic conditions showed a high release of Zn and Cd (10 times the legislative limits), with metals possibly migrating via water infiltration or runoff. Under anaerobic conditions Zn and Cd were initially released. Then, solution concentrations decreased gradually (Zn) or sharply (Cd) until the end of the experiment. Sequential extractions and multisurface modelling indicated that both metals precipitated mainly as carbonates. This was confirmed by a geochemical multisurface modelling, which also predicted the formation of sulphides after 60 days in one soil. The model calculated metals to be preferentially complexed by organic matter and well predicted the observed soil solution concentrations. The results showed that during flooding episodes contaminants could be promptly transferred to other environmental compartments. The use of multisurface modelling coupled with laboratory experiments provided useful indications on the potential release and speciation in case of anoxic conditions. Electronic supplementary material The online version of this article (10.1007/s00244-020-00777-0) contains supplementary material, which is available to authorized users.