Pollution is increasing in the Amazon region and its real impact is still unclear. Since this region is of great interest to the global community, this study aimed to assess geochemical biomarkers and metals in sediments from three streams crossing Manaus, a Brazilian city of 2.1 million inhabitants located in the heart of the Amazon rainforest. The Mindu and Quarenta streams criss-cross the urban area of Manaus and receive domestic effluents from many heavily populated districts. In addition, the Quarenta stream is subjected to effluents from the industrial district of Manaus. The Tarumã-Açu stream is mostly covered by vegetation, although the region presents some occurrence of family farming, floating petrol station, marinas, and floating restaurants and bars. n-Alkanes were determined by Gas Chromatography with Flame Ionization Detection (GC-FID), whereas hopanes and polycyclic aromatic hydrocarbons (PAHs) were determined by Gas Chromatography coupled to Mass Spectrometry (GC-MS). The metals Ag, Cd, Cr, Co, Cu, Mn, Ni, Pb, and Zn were determined by Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES) after microwave-assisted acid digestion. Concentrations of total PAHs and metals were higher in sediments from the urban streams Mindu and Quarenta because of the occurrence of more intense and diverse sources of pollution. In addition, some sediment samples from both these streams presented concentrations of fluoranthene, phenanthrene, and metals higher than the limits of low probability of adverse effects on biota established by the international guideline and by the Brazilian legislation. A similar total n-alkane concentration for sediments from all streams associated with profiles of n-alkanes with no odd/even hydrocarbon predominance suggests that biomass burning is an important source of hydrocarbons. Petroleum-derived products also represented a source for n-alkanes, as confirmed by the presence of α,β-hopanes, including an α,β-homohopane series from C31 to C35 with the presence of both 22S and 22R epimers. This is the first report on n-alkanes, PAHs, and hopanes in sediments from the Mindu, Quarenta, and Tarumã-Açu streams. The concentrations reported herein may be considered as baseline data in future monitoring programs of these streams.