Concentrations of selected antibiotic compounds from different groups were measured in sediment samples (14 analytes) and in near-bottom water samples (12 analytes) collected in 2011–2013 from the southern Baltic Sea (Polish coastal zone). Antibiotics were determined at concentration levels of a few to hundreds of ng g^− 1 d.w. in sediments and ng L^− 1 in near-bottom waters. The most frequently detected compounds were sulfamethoxazole, trimethoprim, oxytetracycline in sediments and sulfamethoxazole and trimethoprim in near-bottom waters. The occurrence of the identified antibiotics was characterized by spatial and temporal variability. A statistically important correlation was observed between sediment organic matter content and the concentrations of sulfachloropyridazine and oxytetracycline. Risk assessment analyses revealed a potential high risk of sulfamethoxazole contamination in near-bottom waters and of contamination by sulfamethoxazole, trimethoprim and tetracyclines in sediments. Both chemical and risk assessment analyses show that the coastal area of the southern Baltic Sea is highly exposed to antibiotic residues.