Five municipal and domestic wastewater treatment plants, most of which had secondary treatment systems formed by activated sludge, were studied during 2013–2014 in Tehran. The study was done in order to evaluate their efficiency in terms of removal of Cryptosporidium and Giardia by (oo)cyst recovery in effluent samples using immunofluorescence with monoclonal antibodies. Results showed that mean concentrations of cysts in the influent samples always outnumbered mean concentrations of oocysts (883.3 ± 4,16.7–3,191.7 ± 1,067.2 versus 4.8 ± 6.2–83.8 ± 77.3 (oo)cysts/L), and that lower concentrations of (oo)cysts were recorded in summer, and higher levels in autumn, and that the difference was statistically significant (t-test, P <0.05) only in wastewater from slaughterhouses. Results for removal percentages of all the plants ranged from 76.7 to 92.1% for cysts and from 48.9 to 90.8% for oocysts. There was more reduction of (oo)cysts at the urban treatment plant by activated sludge-A2O-sand filtration than at plants with conventional activated sludge and activated sludge-trickling filter, however, this difference was not statistically significant for cysts and oocysts (ANOVA, P > 0.05). Infections in mice inoculated with cysts obtained from urban wastewater effluent demonstrated presence of infectious Giardia cysts. Results demonstrate limited efficiency of conventional wastewater treatment processes at physico-chemical removal of (oo)cysts.