This study aimed to analyze the effect of pollution caused by stone quarries on the morpho-anatomy, biochemistry, and physiology of a medicinal wild bramble Rubus plicatus Weihe & Nees. Samples were collected from two natural protected areas: Iron Gates Natural Park and Jiu Gorge National Park, both located in the southwestern part of Romania, and two unpolluted areas from these parks as background sites. We carried out the following analyses on the collected leaves of this taxon: morphology, micromorphology, anatomy, assimilating pigments, heavy metals (Pb, Ni, Cr, Fe), dry mass, bioactive compounds (total phenols and flavonoids), and antioxidant capacity. The results showed more stomata, higher amounts of assimilating pigments, higher amounts of heavy metals (especially lead), less dry mass, less phenols, and more flavonoids in Rubus plicatus leaves from polluted areas compared to areas without sources of pollution. The increased number of stomata and the amounts of assimilator pigments revealed the mechanisms developed by this species in order to survive in polluted conditions.