The goals were to estimate nutrients and carbon flow rates between Guanabara Bay and the adjacent coastal waters, to characterize the provenance of the exported/imported organic matter. Samples were collected from different depths over 25 h in two seasons at the bay entrance. Measurements included physicochemical parameters, nutrients, chlorophylls, dissolved organic carbon (DOC), particulate organic carbon (POC), particulate nitrogen (PN), carbon (δ13C) and nitrogen (δ15N) isotopic composition, sterols in suspended particulate matter (SPM) and bacterioplankton. Most variables showed higher values in ebb tide events. The flow rates calculated on daily basis and estimated on annual basis revealed the exportation to the continental shelf of 1.27 × 104 kmol year-1 dissolved inorganic nitrogen (DIN), 9.52 × 102 kmol year-1 dissolved inorganic phosphorus (DIP), 2.65 × 104 t year-1 DOC, 1.96 × 104 t year-1 POC, and 2.96 × 104 t year-1 PN. The estimates show the bay contributes with 0.01% of the total global carbon influx to the ocean.