Currently, in the Republic of Moldova, due to the high content of biogenic element compounds (namely, nitrogen and phosphorus) in domestic and small-scale industrial wastewater discharged into wastewater treatment plants, necessary measures for the protection of the aquatic environment are required, as these compounds significantly contribute to the eutrophication process of rivers and lakes. To investigate the possibility of intensifying and optimizing wastewater treatment processes in medium-scale plants, tests were conducted based on the newly constructed biological wastewater treatment plant (WWTP) in Causeni, which started operation in 2021. In order to optimize the treatment process, three technological schemes of operation for the Causeni WWTP were modeled. Laboratory investigations of concentration parameters such as CODCr, NO2-, NO3-, and NH4+ were carried out to estimate the processes occurring in each compartment of the WWTP complex and the migration effects of different nitrogen forms. The dynamics of nitrogen form changes throughout the treatment process were also analyzed. The first tested technological scheme involved aeration treatment in four consecutive aeration tanks. The second variant included pre-denitrification in the treatment cycle. For both schemes, organic compound removal and nitrification processes occurred completely, while denitrification took only place in the secondary clarifier. This is deemed unacceptable as it causes process instability with uncontrolled discharge of excess floating sludge. In the third technological scheme, which included pre-denitrification and post-denitrification in the treatment cycle, known as BARDENPHO, an efficiency of 85% in total nitrogen removal was achieved, in accordance with the legal requirements of Government Decision 950. Additionally, the obtained composition complied with the discharge standards into the aquatic environment, with NH4+ at 0.90 mg/dm3 and NO2- at 0.37 mg/dm3. In conclusion, it was demonstrated that aerobic treatment does not significantly enhance the removal effect of biogenic elements. However, the inclusion of anoxic-oxic-anoxic-oxic zones in the sequential biological treatment scheme, along with the use of amplifying selectors, substantially enhances this effect within the same technological volumes, reducing the air consumption for oxidation by utilizing oxygen from nitrate and nitrite compounds.