Silver nanoparticles (AgNPs) are one of the most important nanomaterials for toxicological study due to their extensive use in consumer products and their potential effects on both human and animal health, and the environment. There is, however, insufficient information on their impact on the marine environment. Here, we study the effect of AgNPs in sea urchin (Paracentrotus lividus) development by X-ray absorption near edge structure (XANES) and Fourier transform infrared (FTIR) spectroscopy. Agglomerated AgNPs were observed in sea urchin larva at 51 h after exposure to AgNPs with a concentration of 0.3 mg/L. XANES shows that agglomerated AgNPs contain oxidized Ag species complexed with S and O/N ligands. FTIR results confirm the presence of additional sulphur compounds suggestive of a biological response to the toxicity of AgNPs in the sea urchins. Additionally, it could be concluded from the FTIR results that there is a loss of calcite in the sea urchins exposed to AgNPs.