La Nina events influence the tropical Indian Ocean (TIO) sea surface temperature, sea level and heat content significantly. However, proper quantification in the context of ocean heat transport in the TIO and its persistence is lacking. So, in this study, we have chosen the La Nina events which persist for more than 24-months to study the effects of such events in the TIO using observational and reanalysis data. It is found that prolonged La Nina events promote intensification of cooling anomaly and sea-level-low in the thermocline ridge region of the Indian Ocean (TRIO) and its eastward extension from its climatological location (the southwestern TIO). This happens as a response to the cyclonic wind generated in the southeastern TIO and the associated upwelling Rossby waves which propagate westward to shoal the thermocline in the TRIO region and also extending it eastward while intensifying the cooling and sea level low there. Whereas, in the eastern Equatorial Indian Ocean (EIO) and Bay of Bengal (BoB) a deepening of thermocline, east-west thermocline gradient, anomalous sub-surface warming, increase in the upper ocean heat content and sea-level rise are in the characteristic features of all the prolonged La Nina events. Intense cooling and anomalous sea level low in the Arabian Sea (AS) and intense warming and thermocline deepening in the head bay and the eastward extension of the TRIO regions are found to be unique features of these prolonged La Niña events. These prolonged La Niña events support cross-equatorial Sverdrup transport near the eastern boundary of EIO. This suggests a pathway of warm western Pacific waters accumulated in southeastern EIO entering the north Indian Ocean increasing the heat-content of BoB especially in the 50m—150m depth. The warming (cooling) of the BoB (AS) is speculated to enhance (suppress) pre and post monsoon cyclones over these regions by modulating the tropical cyclone heat potential during these prolonged La Nina events.