Agriculture is key to New Zealand's economy with land-use conversions in response to market forces occurring regularly. Recently, high-intensity dairy farming has replaced low-density livestock farming, often degrading surrounding waterways. Of particular concern is that dairy cattle can be a source of the parasite Giardia, which in humans is a common cause of gastrointestinal infection. Reducing waterway contamination is therefore a priority. The Otago Regional Council has implemented a fencing initiative to physically remove cattle from farmland waterways, eliminating direct contamination by faeces. Our experiment investigated the potential of vegetation barriers planted in conjunction with fences to minimise indirect contamination by runoff. We investigated the pathogen retention potential of three New Zealand grasses soon after planting and after one growing season, in comparison to land recovering from the removal of vegetation. We generated runoff containing non-infectious Giardia cysts and bromide (a conservative tracer) on plots representing the different treatments, collected the runoff, and analysed it for Giardia and bromide. Total bromide concentrations were comparable for all treatments across time, while the degree of Giardia recovered from the four treatments differed over time. These results showed the immediate benefit of vegetation growth in reducing the impact of runoff on aquatic environments.