The free-living amoeba and Acanthamoeba sp. are widely distributed in fresh water, soil, air and dust in the world. We studied distribution of amoeba from low Nakdong River(Mulgum and Maeri) and removal efficiency in water treatment process of Busan metropolitan city. During this investigation, water quality showed pH 7.4～9.6(±1.1), water temperature 2.0～29.0(±17)℃, turbidity 4.8～27.4(±11.0) NTU, chlorophyll-a 10.3～109.0(±44.3) mg/m3, BOD 1.7～4.9(±2.6) mg/L, COD 3.1～6.9(±5.0) mg/L and total coliform 17～920(±200.5) MPN/100 mL. The free-living amoeba were detected highly than Acanthamoeba sp., 11 out of 22 in raw water samples were positive (50%) for Acanthamoeba sp. from February 2005 to December 2005. The seasonal characteristics of free-living amoeba and Acanthamoeba sp. in raw water were mainly distributed through the spring to the early fall. When free-living amoeba and Acanthamoeba sp. were passed through the water treatment of pilot-plant, approximately 80% was sure to be removed through pre-ozonation, sedimentation, send filtration. 100% was removed after post-ozonation process. All of the isolated amoebas from Nakdong River were Acanthamoeba sp. AC311 18S ribosomal RNA gene with 98% nucleotide sequence homology.