The South-east Queensland Ecosystem Health Monitoring Program (EHMP) is a long term (20 years) program that monitors the health of the region’s rivers and streams. Ecosystem health indicators used in the program were selected as they responded predictably to the land-use and vegetation condition of the sampling site and the upstream catchment. This paper describes three analyses that demonstrate how riparian vegetation, both at the site and in the upstream catchment, influences macroinvertebrate indicators of river health, specifically overall Family richness, the richness of PET taxa and SIGNAL score (a measure of pollution sensitivity). The presence of dense riparian vegetation at the site and along the upstream riparian corridor was identified as the most important scale of land-use having a positive impact on macroinvertebrate assemblages. The species composition of this riparian vegetation at the site scale did not influence macroinvertebrate assemblage composition, with structural attributes of riparian vegetation, such as canopy cover, having the dominant control over assemblage composition and ecosystem health. More importantly, when the data was analysed to determine trends in ecosystem health over the 20-year period, the presence of dense riparian cover in the upstream corridor provided a stablising influence on ecosystem health, mediating the more immediate impacts of rainfall, particularly very high and low rainfall periods. Overall, these analyses provide multiple lines of evidence of the importance of healthy riparian zones for maintaining the integrity of stream and river ecosystems.