Acanthamoeba spp. are ubiquitous in both natural and man-made environments and have been isolated in lakes, recreational pools, tap water, and air conditioning systems. Twenty surface water (SW) samples were collected from different sampling areas of Lake Buhi. Water samples were pelleted, cultured in NNA lawned with Escherichia coli and observed microscopically. 10% of samples (2/20) were positive for amoebic growth and were furthered tested using molecular techniques. Polymerase chain reaction showed the presence of Acanthamoeba sp. DNA. The presence of potentially pathogenic Acanthamoeba sp. poses a public health concern. The formulation of policies for proper information dissemination and control measures to avert the contraction of pathogenic FLA as well as other WBPP should be seriously considered.