Our aim was to quantify microplastic ingestion by fish assemblages in two tropical Brazilian estuaries and to evaluate whether biological and ecological factors influence the ingestion of microplastics by fish species. Of 2233 fish from both estuaries (from 69 species) examined in this study, 9% of the individuals (24 species) had microplastics in their gut contents. Microplastic ingestion occurred irrespective of fish size and functional group. The diet of fish species was analyzed based on prey items identified in the fish's full stomach contents and five feeding guilds were defined. Microplastics were common throughout all feeding guilds. Low (average ingestion values 1.06±0.30 items/total fish) but widespread occurrence among estuaries also indicates proliferation of microplastic pollution. Our findings highlight the need to focus on assemblage level studies to understand the real magnitude of the problem and emphasize the urgency of mitigation measures directed at microplastic pollution in estuarine ecosystems. •We analyzed microplastic ingestion in 69 fish species collected along two estuaries.•Microplastic ingestion was widespread in fish assemblages in two tropical estuaries.•Microplastic ingestion was independent of fish size and fish functional groups.•Microplastics were observed in fish from five different feeding guilds.•The level of anthropogenic pressures did not influence microplastic ingestion.