Many biotic integrity indices are not able to isolate community effects due to pesticide exposure as the communities also respond to other anthropogenic and natural stressors. A macroinvertebrate trait bioindicator system that is pesticide specific was therefore developed to overcome these challenges. This system, called SPEAR (SPEcies At Risk), was applied in South Africa as an indicator to link known pesticide catchment usage to changes in the macroinvertebrate community, especially when analytical methods are inconclusive. In addition, the SPEARsalinity index within the SPEAR suite of tools was also evaluated for its effectiveness in South Africa. The results indicated that all of the sites have either been exposed to the same pesticide pressure or not been exposed to pesticides as the SPEAR results were similar when compared to the pesticide intensity. The interaction with other factors like nutrients or salinity was likely a factor that confounded the SPEARpesticides indicator.