One of the most important sources of solid waste in the Mediterranean Basin ecosystem originated from the phosphate fertilizer industries, which discharge phosphogypsum (PG) directly into aquatic environments or are stacked on stockpiles. The present study investigates metal release from PG under the influence of variable pH, increasing PG mass content, and complexing organic matter ligands. Major ions from PG leachates, grain size and charge, main functional groups along with metal leachability (Pb, Cd, Cr, Cu, and Zn) were determined using ion chromatography, laser diffraction, zetameter, Fourier transform infrared spectroscopy, and atomic absorption spectroscopy, respectively. The complete dissolution of PG recorded is at 2 g/L. Saturation and supersaturation with respect to PG may occur at concentrations of 3 and 4 g/L, respectively, revealing a clustering phenomenon leading to heavy metal encapsulation within the aggregates. Organic ligands such as citrate may trigger the cationic exchange within the PG suspension leading to ion release. As these factors are considered as specific process involving the release of contaminants from PG during storage under natural conditions, this study could set the foundations for PG remediation in aquatic environment. Organic ligands under controlled pH conditions could be utilized in treating fertilizer industrial wastes by taking into consideration the particularity of the receiving area, thus decreasing metal hazardous impact on natural media.