In this study, the susceptibility to erythromycin (E) and to trimethoprim/sulfamethoxazole (SXT) among isolates of Enterococcus spp. and Escherichia coli was tested, respectively. Both fecal indicators were detected and isolated from raw (RW) and treated wastewater (TW) as well as from samples of activated sludge (AS) collected in a local wastewater treatment plant (WWTP). Biodiversity of bacterial community in AS was also monitored using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Additionally, distribution of sul1–3 genes conferring sulfonamide resistance was tested among SXT-resistant E. coli. Simultaneously, basic physicochemical parameters and concentrations of eight antimicrobial compounds (belonging to folate pathway inhibitors and macrolides class) were analyzed in RW and TW samples. Six of the selected antimicrobial agents, namely: erythromycin, clarithromycin, trimethoprim, roxithromycin, sulfamethoxazole, and N-acetyl-sulfamethoxazole were detected in the wastewater samples. Bacterial biodiversity of AS samples were comparable with no relevant differences. Among tested Enterococcus spp., E-resistant isolates constituted 41%. SXT resistance was less prevalent in E. coli with 11% of isolates. The genes conferring resistance to sulfonamides (sul1–3) were detected in SXT-resistant E. coli of wastewater origin with similar frequencies as in other environmental compartments, including clinical ones.