Some heavy metals and trace metals reach aquatic ecosystems from natural and anthropogenic sources, and are considered some of the most important environmental contaminants due to their toxicity, persistence and tendency to accumulate in aquatic organisms. Thus, their study is needed due to the environmental risk they pose. Concentrations of Cu, Cd, Mg, Fe and Mn in recent sediments of the deltaic lagoon-river system of the Palizada river, Campeche, Mexico were determined for three climatic seasons on the 2010 annual cycle. The results confirmed that the climatic season has great influence over the results variability. The highest levels of Cu, Fe and Mn were found during dry season, which may suggest significant evaporation phenomena in the area. Both Fe and Mn are abundant elements in the Earth crust; their concentrations could be related to the study area's characteristics, given the conjunction of two sedimentary provinces: terrigenous in the western portion and carbonated in the eastern. On the other hand, the results suggest a high relationship of Fe-Mn (r = 0.5131), Fe-clay (r = 0.5978), Cu-Mn (r = 0.8707), Cu-clay (0.8501) and Mn-clay (0.9311). The latter confirms the high dependence of these elements and the great affinity of some metallic elements for finer sediments. In conjunction, the climatic season and the sediment's characteristics are essential for metal mobilization and transport. Likewise, the Cd and Cu levels reported are lower than international parameter, indicating value ranges that could cause effects in exposed organisms.