Two oceanographic cruises were taken during the winter (SAV I, November and December 2007) and summer (SAV II, July and August 2008) across the mouth of the Papaloapan River in the Gulf of Mexico. Surficial sediment samples were collected from shallow (16-30 m), intermediate (30 to 80 m), and deeper areas (≥300 m). Shallow water sediments are coarser, better-sorted, and primarily composed of sands during the winter, while those found in the summer are finer. At depths greater than 30 m, sediments are primarily fine-grained no matter the season. Major element analysis from shallow areas indicates higher SiO2 concentrations during the windy season with negative correlation against Al2O3 during both seasons, following the respective abundances of sand and muds. High organic carbon content was observed in shallow areas during the summer. Trace metals V, Ni, Cu, Zn, Pb, Li, Cr, Co, and Ba were evaluated. The first six metals showed higher average concentration in the deeper areas, although the highest values at some individual sampling sites for Cr, Co, Cu, and Ba were observed in the coastal area. Factor and cluster analysis were used to explain the sediment distribution pattern and the factors that determine the sediment characteristics within the study area. In shallow areas, four clusters were observed during the winter and five during the summer. The geochemical characteristics of the samples in each cluster suggest association with fluvial sediment input, textural characteristics, heavy minerals, and Cu and Ba concentration. To evaluate the variations in heavy metal concentration, metal enrichment factors (EFs) were calculated. Enrichment in V, Cr, Co, Zn, Ba, and Pb was detected at certain sites, whereas Cu behaved differently. The distribution of Cu enrichment suggests that it may be of natural origin, associated with the lithology of the volcanic continental area. The minor enrichment observed for other elements may be associated with river discharge. According to sediment quality guidelines, trace metal concentrations of Cu, Pb, and Zn present occasional risks to aquatic organisms.