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Purpose Planting strategies can be effective mechanisms to reduce diffuse pollution from agricultural catchments reaching water bodies. Plants with antimicrobial properties such as mānuka (Leptospermum scoparium) demonstrated in controlled conditions the ability to inhibit nitrification and growth of pathogens in soils. This potential in a real on-farm setting was still to be investigated. Methods In a stock-excluded riparian area, planted with mānuka on a dry stock farm, synthetic excrement patches high in urea (950 kg N ha−1 equiv.) and Escherichia coli (7.9 × 109 cfu plant-1) underneath mānuka saplings and pasture were applied. Soil was sampled at three depths over 21 days after the excrement application and analysed for total C and N, inorganic N, pH, soil moisture and E. coli. Results There was no significant difference between the pasture and mānuka for total C and N, C:N ratio, and soil moisture. E. coli was only different between both at 20–30 cm deep. NO3− - N and NH4+ - N concentrations were significantly lower under mānuka compared to pasture for the upper two soil depths (NO3− - N: 109 mg kg−1 vs 205 mg kg−1 in the topsoil). Conclusions The results of this study indicate that mānuka may inhibit urease activity and nitrification and could reduce on-farm nitrate leaching, while also highlighting that field conditions make quantifying such phenomenon more complex.