Display omitted •Toxicological effects of ciprofloxacin on C. mexicana was studied.•96h EC50 of ciprofloxacin for C. mexicana was 65mgL−1.•Ciprofloxacin influenced the biochemical characteristics of microalgal cells.•MDA and SOD of C. mexicana were significantly increased by ciprofloxacin.•Sodium acetate acts as an electron donor and enhanced ciprofloxacin removal. This study evaluated the toxicity and cellular stresses of ciprofloxacin (CIP) and its co-metabolic removal in a freshwater microalga Chlamydomonas mexicana. The toxicological effects of CIP on C. mexicana were assessed by studying the growth and biochemical characteristics of the microalga including total chlorophyll, carotenoid content, malondialdehyde (MDA) and superoxide dismutase (SOD) activity. The calculated effective concentration (EC50) of CIP on C. mexicana was 65±4mgL−1 at 96h. The growth of C. mexicana was significantly inhibited at increased concentrations of CIP, showing 36±1, 75±3. and 88±3% inhibition at 40, 60 and 100mgL−1 CIP, respectively, compared to the control after 11days of cultivation. The total chlorophyll, carotenoid, MDA and SOD activity were significantly increased as a result of relatively high concentrations of CIP stress. C. mexicana showed 13±1% removal of CIP (2mgL−1) after 11days of cultivation; however, the addition of an electron donor (sodium acetate, 4gL−1) highly enhanced the removal of CIP (2mgL−1) by>3-fold after 11days. Kinetic studies showed that removal of CIP followed a first-order model (R2 0.94–0.97) with the apparent rate constants (k) ranging from 0.0121 to 0.079 d−1.