Guanabara Bay, located adjacent to Rio de Janeiro in Brazil, is highly contaminated by substances derived from domestic and industrial effluents as well as from agricultural runoff. In the present work, sedimentary coprostanol and other faecal sterols were used to investigate historical trends in sewage contamination. Sediment cores were collected from eight different (and characterized) locations in the bay and were sectioned into dated segments. Organic carbon was determined by dry combustion and sterols were separated and quantified by GC/MS. The space-distribution of organic carbon and faecal sterol concentrations generally coincided with the presence of known pollution sources. Concentrations of coprostanol as high as 40 μg g−1 were found, indicating areas of severe sewage contamination. Faecal sterol ratios, commonly used as tools to investigate contamination in temperate environments, however, were found to have limited applicability to this tropical estuarine system, probably due to the influence of intensive primary production and microbial processes.