The purpose of this study is to (1) present an overall view of the macroinvertebrate communities along the middle section of the Zayandeh Rud River, (2) determine the biological water quality based on benthic communities, (3) study the application of the BMWP and revised BMWP score systems in the river and (4) to compare the results of the BMWP and revised BMWP with four commonly used non-parametric community structure indices including taxa richness (TR), Margalef’s index (R), Shannon– Wiener diversity index (H) and Simpson’s diversity index (D).