Guanabara Bay is an estuarine environment of great socio-economic importance, where around 12 million people live in its drainage basin. We aim to characterize the sedimentary matter of Guanabara Bay, two mangrove systems therein (Suruí and Piedade mangroves), and the rivers, São João do Merití, Iguaçu, Sarapui, Suruí, and Guapimirim, by performing sedimentological, mineralogical, elemental/isotopic organic matter composition (total organic carbon and total nitrogen, 13C and 15 N) and organic matter petrography. Samples from the entrance of the bay present high values of quartz, low values of C/N ratio, and high percentages of diffuse amorphous organic matter indicating marine influence, whereas samples from rivers mouths present high percentages of translucent lignocellulosic, opaque lignocellulosic, gelified organic matter, and high C/N ratio probably due to the influence of terrestrial organic matter that comes from the drainage basin and the mangroves areas. Stations of the central sector of the bay were characterized by high percentages of TOC, intermediated values of δ13C, low C/N ratio, and also high diffuse amorphous organic matter indicating a predominant influence of organic matter from algae origin. High values of δ15N indicate large assimilation of nitrate or a high denitrification process in the highest productivity areas. In the river mouth regions, it is mainly influenced by terrestrial organic matter; however, in the northwestern and western sectors, organic matter is influenced both by terrestrial and domestic sewage influences which promote anaerobic decomposition of organic matter.