When the concentrations of ampicillin (Amp), atrazine (Atr) and cadmium chloride (Cd) reach excessive quantities, they become toxic to aquatic organisms. Due to the acceleration of the industrialization and the intensification of human activities, the incidence and concentrations of these types of pollutants in aquatic systems are increasing. The primary purpose of this study was to evaluate the short-term effects of Amp, Atr and Cd on the physiological indices and gene expression levels in Microcystis aeruginosa. These three pollutants significantly induced antioxidant activity but continuously accelerated the cellular oxidative damage in microalgae, which suggests an imbalance between the oxidant and the antioxidant systems. Amp, Atr and Cd also decreased the transcription of psaB, psbD1 and rbcL; the lowest transcription of these genes was only 38.1, 23.7 and 7% of the control, respectively. These three pollutants affected nitrogen (N) and phosphorous (P) uptake by inhibiting the transcription of N or P absorbing and transporting related genes, and they down regulated the transcription of microcystin-related genes, which caused a decrease of microcystin levels; and the lowest level of microcystin was only 42.4% of the control. Our results suggest that these pollutants may cause pleiotropic effects on algal growth and physiological and biochemical reactions, and they may even affect secondary metabolic processes.