The spatial distribution of aliphatic and polycyclic aromatic hydrocarbons (PAHs) was investigated in sediments from the Cienfuegos bay. The highest anthropogenic hydrocarbon inputs were found near the city of Cienfuegos with an unresolved complex mixture (UCM) of aliphatic hydrocarbons and alkylated PAHs, indicative of petrogenic inputs. Parent PAHs, which are typical of high-temperature combustion processes, were evenly distributed in the whole basin and largely prevailing in the southern part of the Cienfuegos city. Biomarker fingerprints assign the sources of pollution to mixes of national and non-national crude oils. The overall levels of anthropogenic hydrocarbons are relatively high compared to relevant areas worldwide and reveal a moderate/high level of hydrocarbon pollution. The Cienfuegos bay sediments received over a period of 5 yr, 50 T/yr of petrogenic unresolved hydrocarbons (UCM) and 2 T/yr of PAHs, being deposited the 80% in the sediments of the north basin.