Next to the city of Huelva (SW of Spain), around 100 Mt of phosphogypsum (PG) are stored in stacks on the salt-marshes of the Tinto River estuary covering a surface of about 1000 ha. Due to the high content of 238U series natural radionuclides of the PG, its acidic nature (pH about 3), and the fact that PG stacks were disposed without any kind of isolation from the substrate, they could produce a potential radioactive impact into the underlying sediments. The aim of this work is to assess the pollution of the underlying sediments by natural radionuclides coming from the PG stacks. To this end, seven cores were taken, and PG and sediments samples collected at different depths were analysed. The activity concentrations of the main long half-live natural radionuclides of interest were determined by applying both gamma-ray and alpha-particle spectrometry radiometric techniques. The results of this study showed that the first decimeters of salt-marsh sediment act as a "barrier" for the radionuclides coming from the PG stacks decreasing rapidly its activity concentration in depth, affecting mainly sediments located in the first 20 cm below the contact due to mixing processes. While 230Th, 226Ra and 210Pb pollution is mainly restricted to the first 20 cm of sediments, U-isotopes can reach higher depths (up to around 50 cm) by leaching processes due to their lower reactivity and higher concentration in the polluted leachates. The obtained results have high relevance for the design of the perimeter channel which is projected to build in the restoration project, suggesting that should has around 1 m deep under the base of the PG stacks, to ensure the full collection of polluting leachates, and to prevent their release into the estuary of the Tinto River.