Aiming to investigate the deposition of pollen grains and spores in Guanabara Bay, Rio de Janeiro State, 61 surface sediment samples were analyzed. The results showed that the current deposition of palynomorphs in surface sediments of Guanabara Bay represents the regional vegetation of this hydrographic basin. The differential distribution of palynomorphs followed a pattern influenced by bathymetry, tidal currents speed, discharge of numerous rivers, and by human activity. The dominance of representatives of Field Vegetation reflects the changes of the original flora caused by intense human activities in the region. The continued presence and richness of pollen types of rain forest in the samples indicates that their source area might be the vegetation from riparian border of rivers in the western sector of the Bay, where the mangrove vegetation is being preserved. The large amount of damaged palynomorphs may be related to abrasion that occurs during river transport, indicating removal or reworking from their areas of origin.