Environmental contamination by nanoparticles (NPs) and drugs represents one of the most debated issues of the last years. The aquatic biome and, indirectly, human health are strongly influenced by the negative effects induced by the widespread presence of pharmaceutical products in wastewater, mainly due to the massive use of antibiotics and inefficient treatment of the waters. The present study aimed to evaluate the harmful consequences due to exposure to antibiotics and NPs, alone and in combination, in the aquatic environment. By exploiting some of their peculiar characteristics, such as small size and ability to bind different types of substances, NPs can carry drugs into the body, showing potential genotoxic effects. The research was conducted on zebrafish () exposed in vivo to lincomycin (100 mg/L) and titanium dioxide nanoparticles (TiO NPs) (10 µg/L) for 7 and 14 exposure days. The effects on zebrafish were evaluated in terms of cell viability, DNA fragmentation, and genomic template stability (GTS%) investigated using Trypan blue staining, TUNEL assay, and the random amplification of polymorphic DNA PCR (RAPD PCR) technique, respectively. Our results show that after TiO NPs exposure, as well as after TiO NPs and lincomycin co-exposure, the percentage of damaged DNA significantly increased and cell viability decreased. On the contrary, exposure to lincomycin alone caused only a GTS% reduction after 14 exposure days. Therefore, the results allow us to assert that genotoxic effect in target cells could be through a synergistic effect, also potentially mediated by the establishment of intermolecular interactions between lincomycin and TiO NPs.