Germination and seedling development are crucial processes for plant growth and survival, and asexual propagules are predominant reproduction organs for aquatic plants. Ciprofloxacin is widely detected in both terrestrial and aquatic ecosystems, while studies on its effects on germination and seedling development mainly focused on terrestrial plants. We evaluated effects of ciprofloxacin (0.1, 1, 5 and 10 mg/L) on turion germination and early establishment of two submerged plants species (Potamogeton crispus L and Hydrilla verticillata Royle). Results showed that ciprofloxacin did not impact germination rate and rooting rate of both species. However, 0.1 mg/L ciprofloxacin significantly accelerated germination of H. verticillata while 5-10 mg/L ciprofloxacin significantly delayed rooting process of both species. With rising ciprofloxacin concentrations and prolonging exposure time, seedling tolerance index and root number of both species decreased significantly, and shoot number decreased slightly in P. crispus but kept increasing in H. verticillata, suggesting better tolerance of the later under ciprofloxacin exposure. Root and shoot biomass accumulation of both species was significantly inhibited, which was partially due to ciprofloxacin toxicity on photosynthetic pigments. By integrating the biomarkers including plant antioxidants, lipid peroxidation degree and hydrogen peroxide contents, we found that the holistically toxicological effects of ciprofloxacin on seedlings of both species were enhanced with increasing ciprofloxacin concentrations. Overall, ciprofloxacin impacted turion germination process and harmed early establishment of these two submerged plants, which might suggest adverse effects of ciprofloxacin on the survival and expansion of submerged aquatic plant populations and their restoration effectiveness for degraded aquatic vegetations.