Zirconium (Zr), hafnium (Hf), and niobium (Nb) are incompatible elements concentrated on the granitic continent. They are trace elements at the pmol/kg level in seawater and are considered potential tracers for water masses. However, data on the distribution of the three elements in modern oceans are limited, particularly in the Indian Ocean. Here, we report the first basin-scale sectional distributions of the three elements at 11 stations from 62°S to 17°N in the Indian Ocean and Indian sector of the Southern Ocean. Unfiltered and filtered seawater samples were stored in low-density polyethylene (LDPE) bottles for approximately 12 years and used to determine the concentrations of the total dissolvable (td) and dissolved (d) fractions, respectively. We found that the absorption percentages on the bottle wall were <10% for Zr, Hf, and Nb. The concentration ranges of dZr, dHf, and dNb in the Indian Ocean and Indian sector of the Southern Ocean were 8–348, 0.06–1.06, and 1.3–4.3 pmol/kg, respectively. The labile particulate (lp) concentration was obtained as the difference between td and d, which was less than the detection limit in most samples. The concentrations of dZr, dHf, and dNb in surface water were high in the Bay of Bengal and Arabian Sea, and the concentrations of Zr and Hf in the deep waters of the Indian Ocean were higher than those in the deep waters of the North Pacific Ocean in a similar manner with dAl. These results indicate that the Indian Ocean has strong influences of lithogenic sources for Al, Zr, and Hf. The dZr/dHf mole ratio characterized water masses in the Indian Ocean and increased in the following order: Atlantic Ocean < Indian Ocean < Pacific Ocean due to the preferential removal of dHf over dZr during thermohaline circulation and the local input of dZr and dHf in the Indian Ocean. Thus, we propose that the dZr/dHf ratio is a potential tracer for global ocean circulation.