Benthic macroinvertebrates, the community that lives in the river and coastal, play important role in the transfer of organic materials. This study aimed to determine the diversity of it in Cimandiri river and estuary. Also, to understand the relation between the community with environmental variables. The research was conducted in September and November 2020, which taken from 10 locations at Cimandiri waters. Benthic macroinvertebrates were collected using the Ekman grab sampler with three replications. Moreover, physicochemical parameters of water and sediment were measured. In general, about 35 taxa belonging to six Classes, including Gastropod, Bivalve, Insect, Malacostraca, Clitellata, and Polychaeta have been found during sampling. Furthermore, Stenelmis sp., one of Insects was predominant benthic invertebrates in the river, whereas Tarebia granifera predominated inhabit the estuary. Margalef richness and Shannon-Wiener diversity index in the river area were about 2.69 and 1.47, while in the estuary was around 1.59 and 0.87. Canonical Correspondence Analysis shows that the number of individuals of 25 taxa tended to correlate with water temperature, TDS, salinity, total of nitrate (TN), total of phosphorus (TP), and total of organic matters (TOM). While, 10 other taxa correlated with pH, turbidity, dissolved of oxygen (DO), ammonia, and the total of suspended solids (TSS).