The Santos Estuarine System (SES) is a complex of bays, islands, estuarine channels, and rivers located on the Southeast coast of Brazil, in which multiple contaminant sources are situated in close proximity to mangroves and other protected areas. In this study, the composition and structure of the macrobenthic communities of SES were described and ninetynine species were identified, with the predominance of polychaetes and bivalve mollusks. The benthic assemblages also showed strong signs of stress, as indicated by the low abundance, richness and diversity, and the dominance of opportunistic species. Integrated analysis including sediment characteristics related to natural and anthropogenic factors (e.g., sediment chemistry, and toxicity) indicated that benthic fauna from the inner portions of the SES and vicinities of the SSOS diffusers as Santos Bay were affected. Some locations at the mouths of Santos and Sao Vicente estuaries exhibited moderate disturbance. In other sites from the mouth of S??o Vicente and Bertioga channels, and Santos Bay, the benthic fauna were considered not degraded. Our results suggest that a combination of both environmental factors and contaminants were responsible for the benthic community structure.Funda????o de Amparo ?? Pesquisa do Estado de S??o Paulo (FAPESP)Pr??-Reitoria de Pesquisa - Universidade Estadual Paulista (PROPe-UNESP)Conselho Nacional de Desenvolvimento Cient??fico e Tecnol??gico (CNPq)FAPESP: 98/00808-6; 13/15482-0PROPe-UNESP: 0067/017/13-PROPe/CDCCNPq: 303620/2008-0; 311609/2014-7