A battery of eight biomarkers was applied in the freshwater mussel Dreissena polymorpha to evaluate potential sub-lethal effects of the antimicrobial trimethoprim (TMP, 5-[3,4,5-trimethoxybenzyl]pyrimidine-2,4-diamine). Mussels were exposed for 96 h to increasing concentrations (1, 3, 10 nM) of TMP in in vivo experiments. We determined the single cell gel electrophoresis (SCGE) assay, the micronucleus test (MN test), the apoptotic frequency (Halo assay) and the lysosomal membrane stability (Neutral Red Retention Assay) in mussel hemocytes. Moreover, to reveal whether the oxidative status was altered, measurements of the activity of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and the phase II detoxifying enzyme glutathione S-transferase (GST) were performed using the cytosolic fraction extracted from a pool of entire mussels. The biomarker battery pointed out only a moderate cyto- and genotoxicity on Zebra mussel hemocytes since only a slight increase in DNA damage was registered by apoptosis induction and MN frequency, while significant differences of lysosomal membrane stability from baseline levels were measured at 3 and 10 nM at the end of exposures only. Finally, TMP seems to have a very low induction capability or even an inhibitory effect on the activities of antioxidant enzymes, but a clear significant induction on GST.