Metal wastes can significantly disturb aquatic communities, particularly photosynthetic organisms, the main primary producers in freshwater running ecosystems. In this study, biofilms and diatoms were used as bioindicators to characterize the kinetics of biofilm recovery. An experimental decontamination study was conducted under laboratory conditions, after biofilm colonisation at a site subject to discharge of industrial metals (Zn and Cd) and in parallel at an upstream site, metal-free, considered as a control. After 24 days of colonisation, biofilms were translocated and maintained in the laboratory for 56 days under clean conditions (control and decontamination) or metal contamination. Various tests were conducted from the community level—measures of metal bioaccumulation, cell densities and taxonomic investigations, to the individual level—measures of teratological forms. After 56 days of decontamination, Zn and Cd concentrations in decontaminated biofilms showed a sharp decline, respectively ranging from 6.7 ± 2 to 4 ± 2.5 mg Zn g-1 DW and from 207.6 ± 24.5 to 45.4 ± 9.9 lg Cd g-1 DW. However, at the end of the experiment bioaccumulations remained significantly higher than concentrations in control biofilms. Despite a diatom evolution in biofilm assemblages, taxonomic inventories did not demonstrate a complete restoration of diatom communities in biofilms under decontamination conditions compared with controls, since metal-resistant species initially present after colonisation at the contaminated site, such as Eolimna minima, persisted in high abundance in decontaminated biofilms. Biofilms kept under metal pressure showed very high bioaccumulation capacities and a sharp decline of species diversity which allowed identification of some resistant species. Regarding these first results on the behaviour of diatom biofilms under experimental decontamination conditions, improvement of the natural hydrosystem’s chemical state appears quickly, but an eventual return to good ecological status appears delayed, with the persistence of metal-tolerant species even after 56 days.