Purpose: Texcoco saline lake in Mexico is an important habitat for over 300 species and recharges the Mexico City aquifer. Presently, it is on the verge of disappearance due to increasing anthropogenic pressure and comprises only a few wetland remnants. The impacts of human activities on these wetlands are unknown and uninvestigated. In this regard, this study investigates the degree of metal contamination in this ecosystem during the period of 2015–2018. Materials and methods: Twenty-six sediment samples were collected from nine different wetlands of Texcoco Lake and examined for 17 metals (Al, Fe, Ca, Mg, Na, K, As, Ba, Cd, Co, Cr, Cu, Mn, Ni, Pb, Zn, and Hg) using atomic absorption spectroscopy. The degree of metal accumulation and its ecological risks were evaluated on the basis of several indicators (geoaccumulation index, enrichment factor, sediment quality guidelines, ecotoxicological values, and potential ecological risk index). Furthermore, co-occurrence via multivariate statistical techniques was employed using the measured metal concentrations to identify their possible sources. Results and discussion: The Cd, Cu, Pb, Zn, and Hg sediment concentrations were higher in magnitude than the background North American shale composite values, suggesting their external origin in all studied sediments. According to the calculated enrichment factors and geoaccumulation index, the sediments were mostly contaminated with Cd and Hg. The sediment quality guidelines and ecotoxicological values together with the ecological risk index suggested probable adverse biological effects due to the presence of Cr, Cu, Ni, and Hg. Cadmium and Hg accounted for nearly 51 and 45% of the ecological threat in the sediments. Based on the knowledge about metal levels and co-occurrence in different matrices and the multivariate data analyses of the detected metal concentrations, we infer that the main sources of metals are as follows: (1) Solonchaks and Vertisol soil types (Ca, Mg, Na, and K); (2) urban-industrial effluents from surrounding municipalities and Mexico City (Cu, Pb, and Zn); and (3) industrial discharges of Xalostoc zone (Cd and Hg) near Texcoco. Conclusions: Our results emphasize the impacts of unregulated discharges from municipal, industrial, and metropolitan zones of Mexico City and construction activities for the elevated metal concentrations in the wetland sediments of Texcoco Lake.