The degree of aggregation and/or coalescence of Au-citrate nanoparticles (AuNPs, mean size 21.5 ± 2.9 nm), after delivery in simulated seawater, are shown to be concentration-dependent. At low concentrations no coalescence and only limited aggregation of primary particles were found. Experiments were performed in which the marine bivalve (Ruditapes philippinarum) was exposed to AuNPs or dissolved Au and subsequently, bivalve tissues were studied by Scanning and Transmission Electron Microscopy and chemical analyses. We show that the bivalve accumulates gold in both cases within either the digestive gland or gill tissues, in different concentrations (including values of predicted environmental relevance). After 28 days of exposure, electron-dense deposits (corresponding to AuNPs, as proven by X-ray microanalysis) were observed in the heterolysosomes of the digestive gland cells. Although non-measurable solubility of AuNPs in seawater was found, evidence is presented of the toxicity produced by Au3+ dissolved species (chloroauric acid solutions) and its relevance is discussed. Display omitted ► Limited aggregation for Au-citrate NPs at low concentrations in sea water media. ► Au-citrate NPs are not soluble in seawater after 48 h exposure. ► Gold accumulation is found under exposure of bivalve to AuNPs or chloroauric acid. ► Location of AuNPs at heterolysosomes of digestive gland cells of Ruditapes philippinarum. ► High toxicity of Au3+ dissolved species (chlororauric acid solutions). Concentration-dependent physico-chemical evolution of citrate-stabilized AuNPs in sea water media, and their uptake and sub-cellular location in Ruditapes philippinarum.