Illite-rich sediments from the Laguna Honda wetland, an eutrophicated hypersaline wetland with waters enriched in Mg and Ca surrounded by olive groves in the Guadalquivir Basin River (South Spain), are polluted by elevated concentrations of gold (up to 21.9 ppm) due to agricultural practices. The highest gold contents appear in the shore sediments of the lake, where up to 20 µm homoaggregates of fused gold nanoparticles (AuNp) are found. Small nanoaggregates of up to six fused gold nanoparticles and very few isolated nanoparticles around 1 nm in size can also be observed to form heteroaggregates of AuNp-mica, especially in the deeper sediments in the central part of the wetland, where Au concentrations are lower (up to 1.89 ppm). The high nanoparticle concentration caused by the inappropriate application of pesticides favors nanoparticle collision in the wetland’s Mg- and Ca-rich waters and the fast coagulation and deposition of Au homoaggregates in the gold-rich shore sediment of the lake. The interaction of gold nanoparticles with the abundant illite particles in the wetland’s hypersaline waters promotes the simultaneous formation of low-density Au-illite heteroaggregates, which are transported and deposited in the less-rich-in-gold sediments of the central part of the lake. The small sizes of the isolated AuNp and AuNp-fused contacts of the aggregates suggest modifications in the original nanoparticles involving dissolution processes. The presence of bacterial communities resistant to heavy metal stress (Luteolibacter and Maricaulis), as well as the activity of sulfate-reducing bacteria (SRB) and particularly sulfur-oxidizing bacteria (SOB) communities from the shore sediments, favored the high-Eh and low-pH conditions adequate for the destabilization and transport of AuNp.