The frequency of cyclonic events has increased over the Arabian Sea in the recent past due to the influence of climate change on the Indian Ocean. This study integrates environmental isotopic tracers (δ18O and δ2H) and geospatial data to investigate the occurrence of Cyclone Nisarga during June, 2020, which impacted the Mumbai city, India. High frequency precipitation samples collected during the cyclone exhibited distinctly depleted and widely variable isotopic signatures (δ18O: −15.9‰ to −0.2‰; δ2H: −114.8‰ to 7.5‰; D-excess: 5.7‰ to 15.1‰), compared to the Indian Summer Monsoon (ISM), that is more enriched and having lower variability. These differences are attributed to the dynamic nature of moisture, isotopic fractionation due to organized convective condition and vapour recycling along the trajectory of the Cyclone Nisarga. The structural development and intensification of the cyclone were further examined using Sea Surface Temperature (SST), Outgoing Longwave Radiation (OLR), and wind circulation patterns derived from the HYSPLIT backward trajectory modelling. The elevated SST values and anthropogenic forcing are found to be the key factors responsible for the frequent cyclone genesis and its intensification over the Arabian Sea. The extremely low OLR values and distinct wind patterns are observed during the Cyclone Nisarga. Difference in wind dynamics and clouds patterns between tropical cyclones and the ISM highlight the unique atmospheric and hydro-meteorological processes responsible for the formation of the cyclone. The study offers valuable insights into the mechanisms of extreme rainfall events, aiding in improved forecasting, disaster mitigation, and climate resilience planning in the region.