Predicting nanoparticle fate in aquatic environments requires mimicking of ecosystem complexity to observe the geochemical processes affecting their behaviour. Here, 12 nm Au nanoparticles were added weekly to large-scale freshwater wetland mesocosms. After six months, ~70% of Au was associated with the macrophyte Egeria densa, where, despite the thermodynamic stability of Au in water, the pristine Au nanoparticles were fully oxidized and complexed to cyanide, hydroxyls or thiol ligands. Extracted biofilms growing on E. densa leaves were shown to dissolve Au nanoparticles within days. The Au biodissolution rate was highest for the biofilm with the lowest prevalence of metal-resistant taxa but the highest ability to release cyanide, known to promote Au oxidation and complexation. Macrophytes and the associated microbiome thus form a biologically active system that can be a major sink for nanoparticle accumulation and transformations. Nanoparticle biotransformation in these compartments should not be ignored, even for nanoparticles commonly considered to be stable in the environment.