Heavy metal/loid (HM) pollution of soils, primarily as a consequence of mining and ore-processing activities, poses significant risks to ecosystems and human health. Soil microbial communities play essential roles in maintaining key ecosystem functions, including nutrient cycling, carbon sequestration, and soil stability. The purpose of this study was to characterize the taxonomic composition and diversity of bacterial communities and evaluate their functional adaptation to heavy metal stress in soils affected by long-term gold–copper mining activities in Bulgaria. Ten soil samples representing a Cu pollution gradient (53–860 mg kg⁻¹) were categorized into five pollution classes. High-throughput sequencing of 16S rRNA gene amplicons revealed the dominance of the phyla Pseudomonadota (mean relative abundance 32%), Acidobacteriota (22%), and Actinomycetota (16%). At the class level, Alphaproteobacteria (18%), Terriglobia (16%), and Gammaproteobacteria (14%) were the most abundant taxa, indicating their adaptation to long-term heavy metal contamination. The genus Z2-YC6860 exhibited significant tolerance to Cu, whereas Bradyrhizobium_503372 was negatively associated with As and Zn concentrations. Functional predictions suggested enrichment of key pathways related to heavy metal resistance, including efflux systems and detoxification. The study design spans a broad Cu pollution gradient across river-associated and industrially impacted sites, providing an ecologically relevant framework for evaluating microbial responses to long-term metal stress.