Endocrine disruptors have been widely reported in vertebrates, but their impacts on the ultrastructure of the freshwater invertebrates were not reported. So, this study was designed to investigate the hazardous effects of 0.25 and 2 mg/l concentrations of Bisphenol A (BPA) on the freshwater clam, Caelatura nilotica for 1 and 4 weeks. Biometrics, sex hormones, histology, and ultrastructure of gills and gonads as fundamental tools were investigated. Some biometric parameters increased with exposure and time (Chohen`s d test). condition index, testosterone, and 17β-estradiol decreased significantly with concentration and time (1 and 4 weeks, P ≤ 0.05, ANOVA). Histological examination showed pathological signs which were more severe at 4 weeks than 1 week manifested as necrosis, inflammation, fibrous tissue, and hyperplasia formation, fat droplets accumulations in gills, gonads, and intestine. Scanning electron microscope examination showed erosion of cilia, irregularity, and foci of the gills. In addition, transmission electron microscope examination showed a decrease in protoplasmic enzymes, blebbing (apoptosis) of flagella and degeneration of mitochondria of sperms. In addition, increased yolk granules, fat droplets, gelatinous protection layer and decreased number of microvilli of the oocytes were noticed. So, BPA induced not only hormonal disruption in sex hormones and organs but also caused biometric and gill alterations in the clams which may interfere with bivalves` biology and aquatic environmental conservation. This study also spotted the ultrastructural effects of BPA for the first time in the freshwater clams.