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Macrozoobenthos is a sedentary aquatic biota and is often used as a bioindicator for assessing water conditions. Therefore, this study aimed to investigate the species diversity of the macrozoobenthos and to analyze the heavy metal contamination in Faunus ater in the Rasian and Asahan estuaries in Aceh Province, Indonesia. The sampling was carried out in July 2022 on a squared transect of 1 m × 1 m for the collection of macrozoobenthos samples at random locations. The results showed that there were 17 macrozoobenthos species from both locations, of which 14 species were found in the Rasian River estuary and seven species in the Asahan River estuary. The diversity index of macrozoobenthos was in a moderate category. Terebralia sulcata had a higher density in the Asahan River, while F. ater had a higher density in the Rasian River. The results of the heavy metal analysis in the F. ater sample showed that this macrozoobenthos was contaminated by mercury, cadmium, and lead, of which the concentration of mercury exceeded the threshold limit, and they are, therefore, not safe for consumption.