Bacterial accumulation causes pathological alterations in shellfish tissues. Bivalve cleaning from bacteria is crucial for safe consumption. The present study aimed to evaluate the effect of bacterial depuration on the gill's histology and gill's apoptosis of freshwater bivalves, Spathopsis rubens arcuata. Depuration was applied for one, three, five, and seven days. Microbiological analyses of shellfishes and bacteria specieswere performed. Furthermore, histological investigations and apoptotic marker caspase-3 were examined in the gills of S. rubens arcuata. The results showed that three different bacterial strains; Aeromona, Streptococcus and Bacillus sp. were found in bivalve tissues. Aeromonas and Streptococcus were found three days post-depuration, however, on the fifth and seventh days post depuration, they were undetectable. The percentages of the apoptotic cells in gills decreased in a time-dependent manner during depuration. Gills and gill lamellae exhibited morphological deformations before depuration including degeneration of epithelial cells and connective tissues, haemocytes infiltration and necrosis. Nevertheless, seven days post-depuration, the gill lamellae restored their normal appearance as indicated by parallel gill filaments separated with interlamellar spaces. Collectively, depuration for seven days is crucial to clear bacterial contamination and restore the damaged gill cells into normal status.