The Unare lagoon, Anzoátegui state, Venezuela, serves as a natural sink for inorganic chemical species and organic matter, influenced by continental, atmospheric, and human factors. The present study evaluated the geochemical distribution and fractionation of heavy metals (Cu, Cd, Pb, Ni, Cr, Co, and Mn) in surface sediments and cores by atomic absorption spectrophotometry techniques. The residual fraction of the collected metals was the most important part, followed by the fractions of organic matter, carbonates, as well as exchangeable metals, revealing the trend of less mobile metals. However, they varied with depth and location, reflecting the interaction of hydrodynamic, textural, and human-made processes. The total concentrations determined were: Cu (11.0–73.9 μg/g), Cd (6.21–9.32 μg/g), Pb (61.7–80.7 μg/g), Ni (61.5–92.8 μg/g), Cr (215–315 μg/g), Co (28.7–34.3 μg/g), and Mn (217–586 μg/g), in many cases exceeding the reference values for uncontaminated sediments. The silty texture of the sediments and their high content of organic matter enhance the accumulation of these metals, which, together with the discharge of rivers such as the Unare and the Chávez, fishing activity, maritime traffic, and domestic and industrial discharges, may explain the high content of pollutants in the lagoon. Therefore, the results reflect a growing anthropogenic pressure on this coastal ecosystem, which supports the need for monitoring to mitigate the negative consequences of adverse changes in the environmental management of its biodiversity and ecological function.