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This data article refers to the paper entitled “Multi-element signatures in solid and solution phases in a tropical mixing zone: A case study in the Cai River estuary, Vietnam” (Koukina et al., 2021), which considers the fate of major, trace, and rare-earth elements transported through the estuarine geochemical filter of the typical tropical estuary. The present work contributes to the local geochemical baselines as a background for long-term monitoring of potential hazardous elements. Therefore, the dataset covers the abundance, enrichment, and partitioning parameters of 53 chemical elements in the water, suspended particulate matter, and bottom sediment samples collected in the Cai River estuary and the adjacent part of the Nha Trang Bay (South China Sea) between July and August 2013. The total filtered, particulate, and sedimentary elements were determined by atomic emission and inductively coupled plasma mass spectrometry (ICP-AES; ICP-MS). The environmental indices (the enrichment factor and geoaccumulation index) and partition coefficients were calculated from the total element contents. The data provided is essential for the comprehensive environmental assessment of the anthropogenic impact on the coastal ecosystem as well as for the evaluation and modelling of element fractionation and mobility at the estuarine gradients.