This study was carried out at two different waste-water treatment plants in Quessna activated-sludge and Berkt El-Sabee trickling filters during a period extending between Dec. 2015 and Nov. 2016. Bacterial, protozoan and physico-chemical parameters were investigated monthly at these two plants to elucidate their performance efficiencies in treating and enhancing the waste-water. It was obviously  that protozoa are represented by three main phyla (Sarcodina, Mastigophorea and Ciliophora)  and the ciliated protozoa prevail the other two phyla. The diversity of the  most common protozoan genera was more or less similar where Quessna WWTP has 25 genera (two sarcodines, four flagellates and 19 ciliates), while Berkt El-Sabee plant has 27 ones (three sarcodines, three flagellates and 21ciliated genera). On the other hand, the total protozoan numerical density was higher at Quessna as compared with that of Berkt El-Sabee (30247 organism/L and 25975/L, respectively). The total protozoa , Ciliophora  and Mastiogophorea were proved to be significantly influenced to varying levels with Coliform bacteria  and certain physico-chemical parameters. From the technological point of view, it was proved that the performing efficiency of the activated-sludge in Quessna WWTP is much better than that of  Berkt El-Sabee. Accordingly, it could be possible to recommend the replacing of the trickling filters by the activated sludges to obtain more better wastewater treatment.