Sedimentary, geochemical (total organic carbon TOC, total nitrogen TN, total phosphorus TP, biogenic silica BSi and calcium carbonate (CaCO3) and diatoms data of two sediment cores were used to infer general environmental changes in the northern Gulf of Urabá during the late Holocene. The age models (AMS 14C ) suggested that core of the northeastern margin (SP 9) belong to ~960 years BP, while in the core of the northwestern margin (SP 41) the model was adjusted for the last ~2845 years BP. The results indicated that drilling sites are affected by different hydrodynamic processes that, in general, have been maintained during the late Holocene. While in the northwestern margin oceanic processes dominate and there is low input of fluvial sediments to this site, in the northeastern margin there are processes that favor the transport and accumulation of terrigenous sediments, which limit the growth of diatoms. Between 2845 and 2489 year BP, a higher sea level and wet conditions were recorded in the gulf. Since ~2445 years BP a gradual decrease in sea level allowed delta progradation towards the eastern side of the gulf. Apparently, this process would have intensified its presence in the last ~200 year BP, due to natural and anthropogenic factors. Even though the river discharges are channeled predominantly towards the east side of the Gulf, the trend of increasing TOC and diatoms data suggested fluvial input to the northwestern margin from ~800 years BP, which may be associated with a higher activity of Tarenas mouth, the northern branch of the Atrato River.