Aims: The aims of this study were to determine the efficiency of Kermanshah wastewater treatment plant (conventional activated sludge) and Gilan-e-Gharb wastewater treatment plant (stabilization ponds) in removal of organic matters (BOD 5 and COD), suspended solids, total coliform, protozoan cyst, and parasitic eggs in order to reuse their effluent for agriculture. Materials and Methods: In this study, the samples were taken every five days from both inlet and outlet of wastewater treatment plants (WWTPs) for five months. Identification and counting of the protozoa cysts and parasitic eggs was carried out using McMaster slide according to Bailenger method. Other parameters were determined according to standard methods. Appropriate statistical techniques (T-test, Kolmogorov Smirnov test, and Mann-Whitney U test, Using SPSS ver. 16) were applied to interpret data. Results: The efficiencies of Kermanshah wastewater treatment plant in removing BOD 5 , COD, TSS, total coliform, parasitic eggs, and protozoan cyst were 82 ± 4%, 83 ± 2%, 78 ± 5%, 66.2 ± 4.2%, 97-99%, and 99-100%, respectively. The respective efficiencies for Gilan-e-Gharb stabilization ponds were determined as % 84 ± 3, %82 ± 8, %84 ± 5.3, %75 ± 6, %100, and %100. Conclusions: According to the results, the removal efficiencies of all parameters except COD in stabilization ponds are higher than those in the activated sludge. Effluent quality in both plants met agricultural effluent reuse standards in view of all studied parameters except total coliform.