The impact of urban and agricultural development on sediment quality in the Alvarado Lagoon region in the southern Gulf of Mexico requires an examination of the historical behavior of potential toxic metals (PTMs) and polycyclic aromatic hydrocarbons (PAHs). Consequently, this study aims to assess the ecotoxicological hazards that benthic species and human consumers face in the area. These results are crucial for economic activities in the region and can help prevent future hazards. We examined two sediment profiles from the ecosystem: Profile 1, which spans the period between 1929 and 1998, and Profile 2, which covers the years between 1929 and 2007. The study evaluated the degree of human-induced pollution of six trace metal elements (PTMs): arsenic (As), cadmium (Cd), chromium (Cr), nickel (Ni), lead (Pb), and vanadium (V) in the sediments of Alvarado Lagoon. The Enrichment Factor (EF) and Geoaccumulation Index (IGeo) were computed as internationally recognized indices to measure the magnitude of contamination and additional anthropogenic and geochemical inputs contributing to the natural levels of the elements. Our analysis indicates that there is no evidence of either enrichment or pollution (EF < 1 class 1; IGeo < 0 class zero) found in the sediments of Alvarado Lagoon. The occurrence of these elements can be attributed to their lithogenic origin, as supported by a significant correlation observed between them. Within the 16 polycyclic aromatic hydrocarbons (PAHs) analyzed, solely Naphthalene (Nap) and Phenanthrene (Phe) were identified in both sediment profiles. The levels of chemicals are indicative of minimal ecotoxicological risks, with Nap ranging between 0.25 and 0.43 µg g−1 and Phe ranging between 0.31 and 0.79 µg g−1. The analysis of factors in this study identified two distinct factors, one related to lithogenic processes and another related to petrogenic processes. The sedimentary profiles of the study site confirmed low levels of potentially toxic metals and polycyclic aromatic hydrocarbons (PAHs), posing insignificant environmental risks. As a result, the ecosystem in this area has demonstrated resilience.