This study investigates macrobenthos and corresponding water environmental factors seasonally in middle and lower reaches of Futuan River in Rizhao City, Shandong Province from December 2018 to October 2019, to analyze the composition and biodiversity characteristics of benthic communities and the correlation with water quality factors. The results show that 42 species of benthic animals (14 species of link animals, 20 species of arthropods, and 8 species of molluscs) are identified. The widely distributed species are Limnodrilus hoffmeisteri, Limnodrilus sp. and Chironomus sp. The relationship between total density of benthic animals is spring > winter > autumn > summer. Canonical Correspondence Analysis (CCA) shows a significantly positive correlation between link animals and COD and TP, as well as different correlations between each category and NH₃-N. Biodiversity distribution of benthic animals is related to the structure of river water sources. Water quality is evaluated using biodiversity indicators and water quality biological indicators of indicator species. The results show that Shannon-Wiener index and Margalef index are worse and Pielou index is better, while water quality biological indicators (Goodnight-Whitley index, Bio-pollution index and Wright index) are almost the same with the level of moderately pollution. The evaluation process should consider the objective attributes of rivers and species to obtain a more applicable evaluation management method.