We report the effects of exposure to alkylated silicon nanocrystals ('alkyl-SiNCs' at concentration ~ 7.2 mg/L) and gamma-Fe2O3nanoparticles coated with ultra-thin silica ('SiO2-coated IONPs' at concentration ~ 150 mg/L) on sea urchins Paracentrotus lividus and Arbacia lixula, respectively, studied with X-ray fluorescence (XRF) and Fourier transform infrared (FTIR) spectroscpoies using excitation from a synchrotron light source. A remarkably low mortality and low incidence of skeletal deformation is observed for exposure to both types of nanoparticles studied, despite the high concentrations employed in this work. XRF mapping demonstrates that both types of nanoparticle are found to agglomerate in the body of the sea urchins. FTIR spectra indicates that alkyl-SiNCs remain intact after ingestion and corresponding XRF maps show increased an oxygen throughout the organisms, possibly related to oxidation products arising from reactive oxygen species generated in the presence of the nanoparticles. Exposure to SiO2-coated IONPs is found to produce sulphur-containing species, which may be the result of a biological response in order to reduce the toxicity of the nanomaterial.