This research aimed to indicate mechanisms involved in protection against the imbalanced generation of reactive oxygen species (ROS) during heavy metals (HMs) exposition of Silene vulgaris ecotypes with different levels of metal tolerance. Specimens of non-metallicolous (NM), calamine (CAL), and serpentine (SER) ecotypes were treated in vitro with Zn, Pb, and Cd ions applied simultaneously in concentrations that reflected their contents in natural habitats of the CAL ecotype (1× HMs) and 2.5- or 5.0-times higher than the first one. Our findings confirmed the sensitivity of the NM ecotype and revealed that the SER ecotype was not fully adapted to the HM mixture, since intensified lipid peroxidation, ultrastructural alternations, and decline in photosynthetic pigments’ content were ascertained under HM treatment. These changes resulted from insufficient antioxidant defense mechanisms based only on ascorbate peroxidase (APX) activity assisted (depending on HMs concentration) by glutathione-S-transferase (GST) and peroxidase activity at pH 6.8 in the NM ecotype or by GST and guaiacol-type peroxidase in the SER one. In turn, CAL specimens showed a hormetic reaction to 1× HMs, which manifested by both increased accumulation of pigments and most non-enzymatic antioxidants and enhanced activity of catalase and enzymes from the peroxidase family (with the exception of APX). Interestingly, no changes in superoxide dismutase activity were noticed in metallicolous ecotypes. To sum up, the ROS scavenging pathways in S. vulgaris relied on antioxidants specific to the respective ecotypes, however the synthesis of polyphenols was proved to be a universal reaction to HMs.