Waterway degradation in agricultural settings is caused by direct and diffuse sources of pollution. Waterway fencing focuses on reducing direct faecal contamination, but the extent to which it reduces overland surface runoff of pathogens is unknown. This study evaluated the potential of four riparian treatments to reduce Giardia in saturation excess surface runoff entering the waterway. Treatment 1 comprised exotic pasture grass and weeds that regenerated from bare soil between the fence and the waterway in the absence of cattle grazing and was compared with three others comprising monocultural plantings of New Zealand native grassland plants. Runoff experiments involving Giardia were performed after planting, both prior to and following the summer growing season. Giardia was not detected from any plot prior to cyst addition. In spring the native ‘C. secta’, ‘A. lessoniana’ and ‘C. richardii’ treatments showed significantly greater reductions in Giardia in runoff than the ‘exotic grasses’ treatment, while in autumn the ‘C. richardii’ treatment reduced Giardia more than the ‘exotic grasses/weeds’. A reduction in public health risk should follow from riparian vegetation, whether exotic or native, but with an added benefit in the case of the native tussock grass C. richardii, due to the associated lower runoff rate.