This study examined the influence of fish farming activities on water quality and benthic macroinvertebrates at the Rawang sub-basin of Selangor River. Multivariate statistical techniques were used to determine major influencing water quality parameters causing organic contamination and the dominant pollution-tolerant benthic macroinvertebrates. Sampling was conducted at Guntong River (SR1), Guntong River’s tributary (SR2, the control site), Kuang River (SR3 and SR6), Gong River (SR4), and Serendah River (SR5) using random sampling techniques based on accessibility and proximity to fish farms. Benthic macroinvertebrates and water samples were collected from April 2019 to March 2020. Based on the principal components analysis (PCA), electrical conductivity (EC), dissolved oxygen (DO), biochemical oxygen demand (BOD), chemical oxygen demand (COD), ammoniacal-nitrogen, and total suspended solids (TSS) were major water quality parameters influenced by fish farming activities. The Canonical Correspondence Analysis (CCA) revealed that several taxa of benthic macroinvertebrates (Chironomidae, Naididae, Lumbriculidae, Tubificidae, unidentified Oligochaeta, Leeches (Helobdella sp.), Planorbidae, and some Odonata) were moderately or highly sensitive to TSS, BOD, COD, turbidity, ammoniacal-nitrogen, and EC. These taxa were dominant in the sampling sites, which were close to fish farms. Findings in this study showed that fish farming activities impacted the water quality and benthic macroinvertebrates in this sub-basin.