The study characterized and evaluated the use of the benthic macroinvertebrate community as an indicator of impacts in different estuarine environments around the Industrial Port Complex (IPC) of Vila do Conde (Pará State, Amazon region). Fauna of beaches and rivers, in sectors of the estuary under different degrees of environmental impact (high, medium, and low), was compared in different seasonal periods. Macrofauna was composed of typically fresh-water and estuarine groups. Beaches presented sediment with a texture ranging from medium to coarse sand, with a less rich macrofauna ( = 4.5 ± SE 0.3 taxa/sample) and dense ( = 1,838.1 ± 164.8 ind./m2) of organisms when compared to rivers ( = 5.9 ± 0.3 taxa/sample, and 3,248.9 ± 77.0 ind./m2), which were environments more muddy. For both environments, sites in the high-impact sector were less rich ( = 4.7 ± 0.3 taxa/sample) and dense ( = 2,812.9 ± 232.7 ind./m2) when compared to those in the low-impact sector ( = 7.6 ± 0.4 taxa/sample, and 3,314.3 ± 230.1 ind./m2). Richness ( = 6.4 ± 0.3 taxa/sample) and density ( = 3,859.4 ± 190.2 ind./m2) were higher in the rainier season when compared to the less rainy season ( = 4.8 ± 0.3 taxa/sample, and 1,933.0 ± 172.1 ind./m2). However, there were no significant seasonal changes in composition. Results indicated that the structure of the benthic macroinvertebrate community surrounding the IPC responds to the loss of environmental quality, with extreme effects of a drop in abundance and diversity. Taxa that are more tolerant (Namalycastis caetensis, Cirolana sp., Pseudosphaeroma sp., Tubificidae, and Chironomidae) and sensitive (Hydropsychidae and Eteone sp.) to impact conditions were identified and evaluated as potential bioindicators.