Heavy metals are known for their negative impact on the physiological processes of lichen photobiont. In spite of this, certain lichens are known to be effective pioneers of polluted sites. Cladonia cariosa, C. rei, and Diploschistes muscorum are prominent examples of lichens that spontaneously colonise post-industrial wastes. We examined the effect of total and intracellular Zn, Pb, Cd, As, Cu, and Ni accumulation in the thalli of these species on the physiological parameters of photobiont. Increased accumulation of Zn, Cd, Cu, and Ni in D. muscorum and of Zn and Ni in C. rei negatively affected contents of photosynthetic pigments, whereas concentrations of Pb had a positive effect in all lichen species. Moreover, pigment contents were positively associated with the concentrations of most examined elements in C. cariosa. The results indicate that even if chlorophyll contents reduced, its degradation does not progress. This suggests that metal stress may exert a negative effect on the synthesis rather than on the integrity of chlorophyll. Most importantly, lichen samples of each of the species from polluted sites proved to possess significantly higher FV/FM ratios than those from a reference site; moreover, the contents of elements of lichen thalli positively influenced this parameter. The efficient functioning of the algal component under heavy-metal stress conditions indicates that the examined lichens are well adapted to extremely contaminated substrates.