The increase of swine production in the Pacific Islands has inevitably led to environmental pollution concerns from discharged wastewater derived from both washing and manure. The slurry accumulates in lagoons, where supernatant wastewater containing high levels of pathogens and nutrients becomes nonpoint source water pollution that deteriorates the quality of receiving water bodies. Soil filtration is a promising cost-effective technology for removing pollutants from swine wastewater; however, the excessive growth of bacteria in soil media often accompanies the filtration process. This study investigates soil filtration mediated by protozoa activities to remove Escherichia coli (E. coli) in synthetic swine wastewater. The experiment used plastic columns packed with Leilehua soil from Oahu Island, Hawaii. The soil physicochemical adsorption was seen to reduce 95.52–96.47% of E. coli. However, the average removal efficiencies were increased to 98.17% in a single stage, and 99.99% in two sequential columns, under predation conditions. The filtration media containing naturally established bacterivores with the prey, provided a bioactive means to remove E. coli from the influent. The proper design of Leilehua soil filters potentially removes E. coli from the influent to meet the standard level of recycled water.