Some evidences about the toxicity of heavy metals on phytoplankton communities have been documented; notwithstanding, a little of information about the toxic effects elicited by these toxicants prevails. The study aim was to evaluate the relationships between heavy metals on freshwater phytoplankton communities (FWPC) with biomarkers of the oxidative stress response. Biomarkers of oxidative damage (TBARS, RC=O), antioxidant defenses (SOD, CAT, and GPx), and burdens of Cu, Fe, Mn, Pb, and Zn were measured on FWPC from four artificial lakes and in one natural lake. Relationships with metals and with pH and redox, using principal component analysis (PCA) and redundancy analysis (RDA), were assessed. RDA showed that TBARS and CAT were related to the burden of Fe and with the water levels of Cu in artificial lakes at the beginning of the rainy season. SOD and GPx activities were influenced by loads of Cu, Pb, Mn, and Zn and by the pH and redox from artificial lakes between the months of February and April. By PCA, it was found that oxidation of proteins was similar in the FWPC from ancient lake and semiartificial lake; however, it was not related to the burdens of metals neither to the concentration of heavy metals in the water. On the FWPC from the natural lake, none of the biomarkers under study was related to the burdens or water concentration of heavy metals. Endogenous levels of heavy metals are responsible for the oxidative stress response on the FWPC, particularly, noticeable in the phytoplankton communities from artificial lakes.