The earth is experiencing the impact of climate change due to global warming. Lake ecosystems are no exception and are expected to cope with the consequences of extreme climatic events (hereafter ECE), such as storms, floods, and droughts. These events have significant potential to alter the hydrological characteristics (HC) influencing the physical, chemical, and biological behavior of lake ecosystems. Considering such ecosystem's high-value services and benefits, it is the need of the hour to monitor and evaluate the impact of ECE on lake ecosystems. The second-largest brackish water system in the world, Chilika Lake, situated at the shore of the Bay of Bengal (BoB), has encountered a total of 1306 tropical cyclonic storms in the last 131years. Since most tropical cyclones lead to heavy floods, this could be devastating for the ecosystem and its services. Hence, in order to bridge the knowledge gap, the present study was carried out to understand its impact, based on the available field data of more than two decades (1999 to 2020) and historical records of ECE and HC since 1840 and 1915 respectively from the literature. The study revealed that the ECE attributed to short-term changes in HC which were reflected through an immediate change in trophic state index (TSI, indicator of lake health) and trophic switchover (net autotrophic to heterotrophic) between net sink and source of carbon dioxide (CO2) in specific regions. This study showed that both the ECE as well as a human intervention (opening of the new mouth) had an integrated role in the maintenance of HC within the lake as indicated by the variability of salinity level which is the lifeblood of the Chilika. Major ECE factors which controlled the salinity in Chilika were freshwater input through cyclone-induced flash flooding and seawater exchange through varying mouth conditions, i.e., opening of the new mouth, shifting, and widening of existing mouths due to cyclone impacts. The impact of the cyclone-induced flash flood was sustained for a couple of months to years depending on the magnitudes. As evidenced from the historical data available for ECEs, respective mouth variability, and salinity regime, ECE was found to maintain the salinity regime of the lake in the long run. Since the hydrological characteristics are found to be maintained through ECE as well as human intervention, the Chilika Lake recorded a substantial increase in fishery, seagrasses, Irrawaddy dolphins, migratory birds, and reduction in weed infestation. This study highlights the importance of historical data collection through a continuous systematic lake monitoring program which would enable understanding the ecosystem functioning and behavior with ECE-induced changing environmental conditions which is also a key component for formulating a sustainable management action plan for lake ecosystems around the globe.