The fluvial-lagoon-deltaic system of the Palizada river in Campeche is an ecosystem of socioeconomic and ecological importance. It is justifiable to carry out studies in this system, due to its connection with another larger ecosystem called Términos lagoon. The objective of this investigation was to analyze the concentration of Pb and Cd in sediments of the fluvial-lagoon-deltaic system of the Palizada river and to determine, with this, the contamination index of these metals. Cd presented the highest concentration in sampling sites and climatic seasons with respect to Pb, with a maximum value of 53.926 ± 5.045, while Pb was 10.421 ± 0.218 μg g-1. The same tendency was presented with pollution and geoaccumulation indexes, where the Cd index stands out. The enrichment of heavy metals was identified through the accumulation of Cd and Pb, such process was evaluated through the geoacumulation index (Igeo). The results of this indicated that these elements are contaminating with an anthropogenic origin mainly. This element represents a toxic risk for the Palizada system, due to its high toxicity even at low concentrations, as well as to evaluate the sublethal effects in organisms that inhabit this system and it requires the implementation of an integral monitoring.