The aim of this study was to develop and apply protocols for the microbiological depuration of bivalve molluscs (Chamelea gallina and Mitylus galloprovincialis). The study was divided into the following phases: preparation of two closed-circuit tanks fitted with mechanical, chemical and biological filtration systems for the depuration of bivalve molluscs, mollusc contamination and depuration, analyses of molluscs and depuration waters (biometric and microbiological tests) and statistical processing of the experimental data. The Escherichia coli challenge revealed the high efficacy of the depuration system and thus the possibility of preparing the molluscs for sale in a relatively short period of time. Depuration tests against Salmonella Typhimurium were effective only after 72 h to 84 h. Results for Vibrio parahaemolyticus revealed only a small reduction in the bacterial load during the entire observation period. However, depuration times were shorter in trials with mussels: V. parahaemolyticus was no longer detected after 36 h to 48 h.