Although dissolved concentrations of germanium (Ge) and silicon (Si) in modern seawater are tightly correlated, uncertainties still exist in the modern marine Ge cycle. Germanium stable isotope systematics in marine systems should provide additional constraints on marine Ge sources and sinks, however the low concentration of Ge in seawater presents an analytical challenge for isotopic measurement. Here, we present a new method of pre-concentration of inorganic Ge from seawater which was applied to measure three Ge isotope profiles in the Southern Ocean and deep seawater from the Atlantic and Pacific Oceans. Germanium isotopic measurements were performed on Ge amounts as low as 2.6 ng using a double-spike approach and a hydride generation system coupled to a MC-ICP-MS. Germanium was co-precipitated with iron hydroxide and then purified through anion-exchange chromatography. Results for the deep (i.e. > 1000 m depth) Pacific Ocean off Hawaii (nearby Loihi Seamount) and the deep Atlantic off Bermuda (BATS station) showed nearly identical δ74/70Ge values at 3.19 ± 0.31 ‰ (2SD, n = 9) and 2.93 ± 0.10 ‰ (2SD, n = 2), respectively. Vertical distributions of Ge concentration and isotope composition in the deep Southern Ocean for water depth > 1300 m yielded an average δ74/70Ge = 3.13 ± 0.25 ‰ (2SD, n = 14) and Ge/Si = 0.80 ± 0.09 μmol/mol (2SD, n = 12). Significant variations in δ74/70Ge, from 2.62 to 3.71 ‰, were measured in the first 1000 m in one station of the Southern Ocean near Sars Seamount in the Drake Passage, with the heaviest values measured in surface waters. Isotope fractionation by diatoms during opal biomineralization may explain the enrichment in heavy isotopes for both Ge and Si in surface seawater. However, examination of both oceanographic parameters and δ74/70Ge values suggest also that water mass mixing and potential contribution of shelf-derived Ge also could contribute to the variations. Combining these results with new Ge isotope data for deep-sea sponges sampled nearby allowed us to determine a Ge isotope fractionation factor of -0.87 ± 0.37 ‰ (2SD, n = 12) during Ge uptake by sponges. Although Ge has long been considered as a geochemical twin of Si, this work underpins fundamental differences in their isotopic behaviors both during biomineralization processes and in their oceanic distributions. This suggests that combined with Si isotopes, Ge isotopes hold significant promise as a complementary proxy for delineating biological versus source effects in the evolution of the marine silicon cycle through time.