The exponential development of human activities during the last century has caused a negative impact on all environmental compartments, including coastal areas. Guanabara Bay-SE Brazil has been subjected to significant environmental pollution from increasing urban and industrial development in the last few decades. The major sources of pollution included municipal wastewater, deforestation, urban runoff and industrial effluents. A sediment deposit constitutes a continuous record of the history of a waterbody and its catchment in a chronological sequence, where the information contained in each sediment stratum provides a more or less clearly defined image of a period in the ecosystems history. In the present study, we have investigated the environmental change in the last decades using recent sediments cores along the coastal area of Guanabara Bay. Geochemical trends in coastal sediment depth profiles have been extensively used as indicators of historical pollution, especially when combined with the analysis of biological remains (foraminifera and pollen) in sediments have provided valuable information on respective contribution of terrestrial and anthropogenic inputs into coastal bays. Three sediment cores (~200 cm long) were taken from different areas inside Guanabara bay were interpreted based on sedimentological, foraminifera, pollen, geochemical and historical data for the last 5000 years. High concentrations of metals (Pb, Ni, Cu, Cr, Zn and Mn) were observed in the three sediment cores over approximately the last hundred years. This is also matched by an increase over time in the foraminifera species Ammonia tepida and a decline in the species Buliminella elegantissima. A. tepida is commonly found in restricted and highly polluted environments, whereas, B. elegantissima is more sensitive to environmental deterioration. Pollen analysis shows a gradual decrease in forest and mangrove vegetation since the European settlement and an increase in field vegetation that has accelerated in recently, together with the introduction of exotic species.