The effects and interactive effects of different nitrogen (N) sources (ammonium, nitrate, and urea) and carbon dioxide (CO2) concentrations were investigated on Alexandrium tamarense, a harmful marine dinoflagellate, by measuring its growth (μ), extracellular carbonic anhydrase (CA), and its toxicity to zebrafish (Danio rerio) embryo. The μ and CA were influenced more strongly by CO2 concentrations rather than by N sources; significant effects of CO2 on μ and CA were observed under low CO2 concentration (LC) conditions compared to high CO2 concentration (HC) conditions. The ammonium and nitrate media under LC conditions had the maximum μ and CA, which was inhibited under HC conditions. The embryotoxic effects were influenced more strongly by the N sources than by CO2 concentrations, thus excluding the lower deformation in urea under HC conditions. Moreover, the antioxidant enzymes superoxide dismutase (SOD), glutathione peroxidase (GPX), glutathione S-transferase (GST), and catalase (CAT) were detected in normal (untreated) zebrafish embryos, and among them, the level of SOD was the highest. In summary, this study provides a clear insight for understanding the effects and interactive effects of N sources and CO2 concentrations on the growth and toxicity of harmful dinoflagellates.