Estuaries are considered receptors of various contaminants released into the environment, including Polycyclic Aromatic Hydrocarbons (PAH), a ubiquitous contaminant. In this study, the response of subtidal macrofauna in the polyhaline zone of three tropical estuaries was analyzed using a taxonomic approach, multimetric indices, and functional traits, to three different levels of PAH. The estuaries presented distinct degrees of contamination, with PAH directly correlated with mud percentage and organic matter. The considerable variation in granulometry found in the three studied estuaries may indicate complex hydrodynamics, with very different sedimentary characteristics. The community structure showed typical estuarine characteristics, with low diversity and high dominance. The macrofauna was distinct among estuaries, with no shared dominant species and with several species occurring just in one site, with different compositions, although other parameters of the community structure were similar. The AMBI and functional indices performed better than taxonomic indices in separating the areas with different impacts. In the analyzed communities, the functional traits approach demonstrated consolidated patterns in the estuarine environment, such as the predominance of opportunistic species, generally of smaller size and detritivore/depositivore, under conditions of pollution by the organic load. Local characteristics, such as the predominance of suspensivore organisms and relatively more mobility in areas with higher hydrodynamics, provide insight into the community's behavior on natural and anthropogenic stressors. The multivariate taxonomic and functional analyses were complementary, emphasizing the importance of integrating them in these environments diagnosis. Stressed environments need information from the entire data set for a correct assessment of the community.