The Tethys Ocean was compartmentalized into the Mediterranean Sea and Indian Ocean during the early Miocene, yet the exact nature and timing of this disconnection are not well understood. Here we present two new neodymium isotope records from isolated carbonate platforms on both sides of the closing seaway, Malta (outcrop sampling) and the Maldives (IODP Site U1468), to constrain the evolution of past water mass exchange between the present day Mediterranean Sea and Indian Ocean via the Mesopotamian Seaway. Combining these data with box modeling results indicates that water mass exchange was reduced by ~90% in a first step at ca. 20 Ma. The terminal closure of the seaway then coincided with the sea level drop caused by the onset of permanent glaciation of Antarctica at ca. 13.8 Ma. The termination of meridional water mass exchange through the Tethyan Seaway resulted in a global reorganization of currents, paved the way to the development of upwelling in the Arabian Sea and possibly led to a strengthening of South Asian Monsoon.