Macroinvertebrates have been widely used in freshwater ecosystems as surrogates to assess the impacts of waste discharges and water pollution. However, often interpretations have been made on the impact of one pollutant in the presence of others that may provide an unidentified additive effective or otherwise confound the results. There have been few opportunities to study the impact of pollutants without such potentially confounding effects. We studied macroinvertebrates using a replicated kick sampling technique and identified to the family level to assess and compare the effects of zinc-rich coal-mine waste and organic pollution from treated sewage on an otherwise clean upland stream network within a world heritage area. We used multivariate analysis of macroinvertebrate assemblages from polluted and clean sites to measure and compare the effect of each waste impact to community structure. We also calculated three widely used biotic indices (Ephemeroptera, Plecoptera and Trichoptera (EPT) family richness, family richness, and abundance) and found that the EPT index was the only one to respond to both pollution types. Macroinvertebrate abundance was an important attribute of the study, with each source of pollution having a contrasting effect on total abundance. It also helped us to measure the relative response of families to each pollutant. There was an initial significant modification of macroinvertebrate assemblages below the outflow of each of the pollutants, followed by different degrees of recovery downstream.