Residues of veterinary antibiotics are a worldwide problem of increasing concern due to their persistence and diverse negative effects on organisms, including crops, and limited understanding of their phytotoxicity. Therefore, this study aimed to compare the phytotoxic effects of veterinary antibiotics tetracycline (TC) and ciprofloxacin (CIP) applied in a wide range of concentrations on model plant oilseed rape (Brassica napus). Overall phytotoxicity of 1–500 mg kg−1 of TC and CIP was investigated based on morphological, biochemical, and physiological plant response. Photosystem II (PSII) performance was suppressed by TC even under environmentally relevant concentration (1 mg kg−1), with an increasing effect proportionally to TC concentration in soil. In contrast, CIP was found to be more phytotoxic than TC when applied at high concentrations, inducing a powerful oxidative burst, impairment of photosynthetic performance, collapse of antioxidative protection and sugar metabolism, and in turn, complete growth retardation at 250 and 500 mg kg−1 CIP treatments. Results of our study suggest that TC and CIP pollution do not pose a significant risk to oilseed rapes in many little anthropogenically affected agro-environments where TC or CIP concentrations do not exceed 1 mg kg−1; however, intensive application of manure with high CIP concentrations (more than 50 mg kg−1) might be detrimental to plants and, in turn, lead to diminished agricultural production and a potential risk to human health.