Historical documentary accounts from the Indian subcontinent document several decade-to-multidecade clusters of severe Indian summer monsoon (ISM) droughts over the past millennium. Many of these putative droughts have no counterparts in the observational period, but an objective assessment of the severity, duration, frequency, and spatial extent of these droughts and their causal mechanisms remains uncertain. Here, we use the Paleo Hydrodynamics Data Assimilation (PHYDA) product to bridge this gap. PHYDA reproduces historical intervals of increased drought frequency with high fidelity and reveals multiple instances of multi-year “black swan” droughts that are in line with historical accounts. We find that droughts, as well as extended periods of dryness, occurred under both El Niño and non-El Niño conditions, with El Niño explaining ~ 49% of all drought instances. A large portion (~40%) of non-El Niño type droughts were likely forced by cooler extratropical SST anomalies in the North Atlantic region. The remaining droughts, however, cannot be accounted for by any other modes of SST, implying a substantial role of ISM internal stochastic variability in driving droughts. While El Niño was an important driver, its association with droughts varied considerably, accounting for between 15-80% of droughts depending on the century. The millennial length perspective afforded by PHYDA supports expanding the El Niño-centric paradigm of ISM droughts into a framework that includes extratropical teleconnections.