The effects of environmentally relevant bisphenol A (BPA) concentrations (0.3, 1 and 3 μg L−1) were tested at 2, 4, 6 and 8 days, on intermediate leaves, of the seagrass Cymodocea nodosa. Hydrogen peroxide (H2O2) production, lipid peroxidation, protein, phenolic content and antioxidant enzyme activities were investigated. Increased H2O2 formation was detected even at the lowest BPA treatments from the beginning of the experiment and both the enzymatic and non-enzymatic antioxidant defense mechanisms were activated upon application of BPA. Elevated H2O2 levels that were detected as a response to increasing BPA concentrations and incubation time, led to the decrease of protein content on the 4th day even at the two lower BPA concentrations, and to the increase of the lipid peroxidation at the highest concentration. However, on the 6th day of BPA exposure, protein content did not differ from the control, indicating the ability of both the enzymatic and non-enzymatic mechanisms (such as superoxide dismutase (SOD) and phenolics) to counteract the BPA-derived oxidative stress. The early response of the protein content determined that the Low Effect Concentration (LOEC) of BPA is 0.3 μg L−1 and that the protein content meets the requirements to be considered as a possible early warning “biomarker” for C. nodosa against BPA toxicity.