A first detailed study of phosphogypsum (PG) from a stockpile in Barreiro (Portugal) was performed aiming for a better characterization of this industrial waste deposit, considering its enhanced content in natural radionuclides and toxic metals, making it a potential contamination source to the Tejo estuary. Whole samples and aggregates of these wastes resulting from phosphate industries were analysed by neutron activation, gamma-spectrometry, X-ray diffraction and scanning electron microscopy. This work clearly shows that a significant chemical heterogeneity in the PG occurs due to the existence of aggregates with different compositions randomly distributed. Among these aggregates, the dark grey ones have high concentrations of Sc, Cr, Zn, Ga, Ba, REE, Ta, W, Th and U and the highest concentrations of 226Ra and 210Pb. The separation of these dark aggregates prior to any application of the PG would lead to a safer reuse of these wastes. The chemical patterns, including the REE distribution with a significant negative Ce anomaly, found in PG, are certainly related with the geochemical signatures of the phosphate rocks used as raw material. This PG stockpile may play a significant role as a radioactive source in the Tejo estuarine environment.