Among plastic additives, bisphenol A (BPA), used mainly in manufacturing objects of everyday use, has received considerable attention for acting as a xenoestrogen and causing endocrine disruption. We now observe its rapid replacement with analogue compounds with similar structures (BPs) whose safety is not fully demonstrated. The present paper investigates the possible adverse effects of BPA, BPF, and BPS on DNA integrity of two gammarid species, Echinogammarus veneris and Gammarus aequicauda, to assess the environmental risk posed by these compounds in the aquatic ecosystem. Moreover, we analysed the cell-specific sensitivity to BPs using somatic (hemocytes) and germ (spermatozoa) cells that could have wide-ranging implications for their reproductive biology and long-term adverse effects at the population level. Results demonstrate that BPA and its analogues caused a genotoxic impact and highlighted lower genotoxic damage induced in sperm cells in both species tested. The implications of the findings of this study on the aquatic ecosystem are discussed, taking into account the critical role of amphipods within the freshwater trophic chain.