Ensuring effective disinfection of wastewater remains a critical challenge for environmental protection and public health under the new European Directive for wastewater 2024/3019. This study evaluates how conventional treatment processes impact the removal efficiency of microorganisms. Standard treatment steps were assessed, including mechanical processes such as primary sedimentation and coarse screening, biological oxidation, and secondary clarification, to determine their role in reducing both microbial contamination and organic and inorganic loads. The research focused on measuring the removal efficiency of suspended solids, ammonium, chemical oxygen demand (COD-Cr), biochemical oxygen demand (BOD₅), total nitrogen, total phosphorus, and microbial populations (fungi, mesophilic bacteria, total and faecal coliforms, fecal streptococci, and selected pathogenic bacteria) at three key points: influent, post-biological treatment, and final effluent. Results showed that microbial removal efficiencies at the final discharge stage ranged from 89% to 100%. Despite these high removal rates, a notable proportion of microorganisms still reached natural receiving waters, potentially impacting aquatic ecosystems and public health. This highlights the need for implementing more effective and environmentally sustainable disinfection methods in the final treatment stage. The findings provide a foundation for further research aimed at optimizing disinfection strategies in relation to influent characteristics, operational control, and compliance with environmental safety requirements.