Headwater streams can constitute up to 80% of river channel length and are vulnerable to anthropogenic pressures due to their high connectivity to adjacent land, large relative catchment size and low dilution capacity. In these environments unrestricted cattle access is a potential significant cause of water quality deterioration, resulting from increases in stream bank erosion, riparian damage and sediment deposition among others. Several studies have reported improvements in physico-chemical and hydromorphological conditions of streams following elimination of cattle access; few, however, have focussed on the ecological impacts of such management practices. Here, such impacts are assessed. We look at the short-term effects by comparing habitat condition, sediment deposition, and instream macroinvertebrate communities upstream and downstream of cattle access points prior to, and one year following exclusion via fencing. The long-term effects are also measured by reassessing a small stream catchment entirely fenced off from cattle access in 2008 under a concerted management effort. In the short term, cattle exclusion led to reduction in deposited sediment downstream of cattle access points and a related homogenisation of macroinvertebrate community structure between upstream and downstream sampling points. Increased abundances of specific indicator taxa ( Ancylus fluviatilis, Glossosomatidae and Elmidae) in the fenced catchment following 9 years of exclusion highlight the long-term ecological benefits of such mitigation practices. These findings highlight the importance of incentivised agri-environment schemes in reducing the negative impacts of cattle access to these vulnerable ecosystems.