A method for the speciation analysis of the three main species of germanium in environmental waters, namely inorganic germanium (iGe), monomethyl germanium (MMGe) and dimethyl germanium (DMGe), has been developed. Germanium species were volatilized by hydride generation (HG) prior to their preconcentration/separation in a semi-automated cryogenic trap (cryotrapping, CT) and detection by ICP-MS/MS. A procedure to minimize the iGe blanks from the chemicals and water is reported. One mL of water can be analyzed without any pretreatment. After application of this procedure, and the careful optimization of all experimental variables, limits of detection (LOD) of 0.015, 0.005 and 0.003 ng L−1 have been obtained for iGe, MMGe and DMGe, respectively. Standard addition experiments did not show any significant matrix effect, and, therefore, external calibration was used for sample analysis. In the Tris-HCl + L-Cysteine reaction media, additional experiments did not reveal any significant demethylation of MMGe to iGe in the process of HG-CT, which could affect the accuracy of the analysis in seawater. The method has been applied to the analysis of iGe, MMGe and DMGe in certified reference materials of unspiked natural waters: CASS-4, CASS-5 and CASS-6 (nearshore seawater); NASS-5 and NASS-7 (seawater); SLRS-4, SLRS-5 and SLRS-6 (river water).