Manure application or wastewater use as irrigation water introduces agriculture as one of the main culprits of spreading antibiotic-resistant pathogens to the environment that threatens human health. Therefore, urgent measures are needed to control the fate of antibiotic-resistant enteropathogens of agricultural origin in the environment. This study aimed to evaluate the effect of different amounts of nano-zeolite on the transport of nalidixic acid-resistant Escherichia coli strain (E. coli NAR) through disturbed soil columns amended with cow manure. Soil mixtures were prepared by adding nano-zeolite (0, 5, and 15%), with/without 5% cow manure to a loam soil. Mixtures were incubated for 60 days and then poured into polyvinyl chloride cylinders (3.6 × 15 cm) for the leaching experiment. After establishing a steady-state unsaturated flow condition, a pulse (0.1 pore volume) of E. coli NAR suspension (106 CFU mL- 1) was added on top of the soil columns. The leaching experiment was followed until 5 pore volume. Nano-zeolite application increased the filtration coefficient (λf), and relative adsorption index (SR), and decreased the maximum depth (Zmax) of E. coli NAR transport in all treatments. Meanwhile, cow manure application increased E. coli NAR transport through soil columns compared to the controls. The average (Cav) and cumulative (Ccum) cell density of E. coli NAR for the columns containing 5% and 15% nano-zeolite were about 2.3 and 10-fold less than the control respectively. Therefore, the nano-zeolite application can improve soil adsorption parameters, even in manure-amended soils, and consequently reduce the risk of groundwater contamination by fecal bacteria.