Ciprofloxacin (CIP) is widely used broad-spectrum antimicrobial drug of fluoroquinolone family. The widespread use of ciprofloxacin increases its release into the environment. Ciprofloxacin is detected in aquatic ecosystems potentially harming aquatic organisms. The CIP effect on photosynthetic organisms is not fully studied. In this study we examined the CIP effect on green freshwater microalgae Scenedesmus quadricauda (Turp.) Bréb. using chlorophyll fluorescence methods (JIP test parameters and rapid light curves). A significant decrease in the cell number was observed at ≥10 mg/L of сiprofloxacin in comparison with control. Analysis of chlorophyll fluorescence parameters obtained from OJIP transients revealed the changes in photosynthetic reactions in сiprofloxacin treatment. Ciprofloxacin was found to inhibit electron transport rate in photosystem II (PSII). The decrease in the quantum yield of electron transport in photosystem II (φEo) was accompanied by the decrease in performance index (PIABS) and an increase in energy dissipation (DI0/RC). Ciprofloxacin enhanced the photosensitivity of microalgae but did not inhibit the recovery of photosynthetic activity after the photooxidative stress. In this regard the effect of CIP differs from that of the well-known antibiotic chloramphenicol that inhibits the resynthesis of plastid proteins and, accordingly, the recovery of photosynthetic activity associated with the resynthesis of PSII protein D1. Among the fluorescence parameters, PIABS was found to be the most stress-specific; therefore it can be proposed to detect an early toxic CIP effect in microalgae.