The aim of this study was to determine the effects of physicochemical parameters and macrophyte on the macroinvertebrate assemblages in the Ketar River, which drains into Lake Ziway. Six sampling sites were selected along the river stretch and samples were collected from December to April 2017/2018 based on the method outlined in Ontario Benthos Biomonitoring Network Protocol Manual. A total of 5,450 individuals comprised of one class, 7 orders, and 23 families were collected during the study period. Hemiptera families were the predominant taxa and contributed the largest percentage of the total samples followed by the Coleoptera. Notonectidae and Corixidae shared the highest total abundance. This study confirmed that the sites covered with macrophytes were significantly different from the substrate both in taxa richness and total abundance (P < 0.05). Redundancy Analysis revealed that pH, Temperature, electric conductivity, DO, NO2, NO3, NH4, SiO2 and TP were the most important variables explaining the variation in macroinvertebrate assemblage patterns. The mean Shannon diversity index also indicated that the sites covered by the macrophyte stand had a significantly higher value than the sites sampled from the substrate, which implies that macrophytes support abundant, and promoting the diversity of macroinvertebrates. Thus, the conservation of macrophytes can enhance the conservation of macroinvertebrates along the course of the river, besides the role of macrophyte in sediment trapping and reducing sedimentation buildup in Lake Ziway.