The present study aims to assess the environmental quality of six estuaries in north-eastern Brazil, using biochemical composition and quantity of organic matter in tropical sediments. Samples were collected monthly during spring low tide from August 2011 to July 2012, in the mid-littoral. Concentrations of organic matter and its biochemical composition reflected the degree of anthropogenic pressure. Although total concentrations of proteins and carbohydrates were similar among estuaries with contrasting levels of anthropogenic pressure, the protein to carbohydrates (PRT : CHO) ratio effectively reflected the trophic state of these areas. PRT : CHO ratios >1 were observed in all studied areas suggesting eutrophic conditions or an initial stage of eutrophication in all of them. Low Chl-a/Phaeo ratios may be associated with the level of eutrophication of each area, however it may also reflect the natural productivity or the presence of mangrove debris. These results were compared with those obtained in previous environmental assessments of the same estuarine areas using the AZTI Marine Biotic Index and monitoring reports showing good agreement. The present study confirmed for the first time in tropical estuarine areas that the biochemical approach can be successfully used to assess the trophic state of the benthic compartment.