Three sediment cores (50 cm depth) were collected at three different sites from a tidal flat estuary at Passagem Channel (Vitória, Espírito Santo State-Brazil) to evaluate the influence of recent urbanization processes on the deposition of organic matter (OM) in a complex polluted tropical estuary. In addition to geochronology (by excess 210Pb), the sources of natural and anthropogenic OM to the sediments were evaluated by total organic C (TOC – 14.29 ± 8.73, 30.43 ± 14.71 and 48.70 mg g−1 ± 25.46, respectively, for P1, P2 and P3), C/N molar ratio and lipid biomarkers (sterols and terpenoids). Taraxerol (3.10 ± 4.85, 9.71 ± 3.85 and 16.10 mg gTOC−1 ± 32.48 for P1, P2 and P3, respectively) and sitosterol (1.71 ± 2.72, 2.94 ± 6.41 and 4.07 mg gTOC−1 ± 4.41 for P1, P2 and P3, respectively) were the most abundant compounds in all cores, suggesting a major contribution of terrestrially-derived OM to the study region. Coprostanol levels and selected sterol index indicated significant contamination by fecal material. The organic geochemical indicators suggest that changes of OM reflect occupation and urbanization alteration processes around the Passagem Channel over the last 70 a, mainly the conversion of mangrove forest into urban areas, bridge building and Treatment Plant Station installation.