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The vertical distribution pattern and concentrations of elements (Fe, Al, Ca, Mg, Mn, Cr, Cu, Ni, Co, Pb, Zn, and As) in the estuarine and lagoon region of Marquelia coast, Guerrero, Mexico, were studied to comprehend the origin and pollutant phases of geochemical elements. Henceforth, two sediment core samples [C1 (127 cm) and C2 (110 cm)] were collected to assess the pollution status using geochemical indices, namely anthropogenic factor (AF), enrichment factor (EF), and geoaccumulation index (Igeo). Additionally, the elemental concentrations were compared with the sediment quality guidelines (SQGs) to examine the potential risks to biota. Among the two depositional environments, the sediments of lagoon Apozahualco exhibited higher concentrations of elements. The granulometry characteristics of sediment grains also attested that the concentration and mobilization of metals are largely governed by the fine-grained fractions. Major elemental concentration and grain size changes were identified at several depths (30–40, 60–70, and 90–100 cm) revealing the internal hydrodynamic condition. The overall assessment of geochemical indices revealed that the sediments were unpolluted to moderately polluted. The anthropogenic factor indicated that the upper portion of the sediments were affected by anthropogenic influences. The comparison of trace element concentration with SQGs denoted that Cr, Ni, and As could pose potential adverse effect to the organisms that live in and near the sedimentary environment. Factor analysis revealed the origin and behaviour of the studied elements during transportation and deposition processes in both the ecosystems (i.e. estuary and lagoon). The results of this study provided an in-depth understanding of variations in elemental concentration and pollution status of sediment profile in coastal transitional environments that would aid in sustainable management. [ABSTRACT FROM AUTHOR]