The aim of this work was to explore the impact of the wastewater discharge from two local pharmaceutical industries on the recipient freshwater environments, particularly regarding the development and spread of antibiotic resistance and bacterial communities composition. Chemical analyses confirmed relatively high antibiotic concentrations in the wastewater from those industries and considerably higher antibiotic concentrations in recipient sediments downstream from the discharge site when compared with upstream reference site. Functional metagenomics revealed already known and potentially novel genes for resistance to targeted antibiotics in wastewater and sediments. Significantly higher concentrations of selected resistance genes were found in sediments at the disharge site and downstream from the pharmaceutical industries discharge site relative to the upstream reference site. Exogenous plasmid isolation revealed the increased horizontal transfer of macrolide and/or tetracycline resistance genes in antibiotic-polluted sediments. Phylogenetic analysis confirmed high similarity of the nucletiode sequences of the ermB gene between environmental bacterial isolates that originated from highly macrolide-polluted river sediments and clinical streptococcal isolates indicating potential transfer of this gene between bacteria of environmental and clinical origin. Sequencing of 16S rRNA gene amplicons revealed significant spatial and seasonal changes in bacterial communities composition of wastewater-exposed sediments. The results of this study highlight the problem of environmental pollution with pharmaceutical wastewater, which may pose a potential threat to both human and environmental health.