Free-living amoebae species, such as Acanthamoeba and Vermamoeba vermiformis are found worldwide and cause severe infections in humans. In the present study, inlet and outlet water samples (n = 96) were collected from conventional and compact drinking water treatment facilities (DWTF), concentrated through nitrocellulose membrane filters (0.45µm pore size), and cultured on non-nutrient agar covered with dead Escherichia coli. The morphologically positive Acanthamoeba and Vermamoeba isolates were subjected to molecular identification and 19 morphologically different Acanthamoeba and two Vermamoeba isolates were genotyped for further confirmation. The results revealed that the predominance free-living amoebae species in surface water samples were belonging to Acanthamoeba (68.8%). All morphologically positive samples for Acanthamoeba proved to be positive by PCR. The conventional DWTF showed better results (66.7%) for removing Acanthamoeba and Vermamoeba vermiformis than the compact DWTF (50%). At the sequence level, three Acanthamoeba genotypes (T3, T4, and T15) and one Vermamoeba species (i.e., Vermamoeba vermiformis) were obtained. In conclusion, conventional DWTF was more effective than compact DWTF in removing Acanthamoeba. The presence of viable Acanthamoeba strains especially the pathogenic types (e.g., Acanthamoeba T4) in outlet water could cause health hazards to consumers.