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In the modern era, due to urbanization, industrialization, and anthropogenic activities in the catchment, greenhouse gas (GHG; CO2, CH4, and N2O) emissions from freshwater ecosystems received scientific attention because of global warming and future climate impacts. A developing country such as India contributes a huge share (4% of global) of GHGs from its freshwater ecosystems (e.g., rivers, lakes, reservoirs) to the atmosphere. This is the first comprehensive review dealing with the GHG emissions from Indian freshwater bodies. Literature reveals that the majority of GHG from India is emitted from its inland water, with 19% of CH4 flux and 56% of CO2 flux. A large part of India’s gross domestic product (GDP) is manipulated by its rivers. As a matter of fact, 117.8 Tg CO2 year−1 of CO2 is released from its major riverine waters. The potential of GHG emissions from hydropower reservoirs varies between 11–52.9% (mainly CH4 and CO2) because of spatio-temporal variability in the GHG emissions. A significant contribution was also reported from urban lakes, wetlands, and other inland waters. Being a subtropical country, India is one of the global GHG hotspots, having the highest ratio (GHG: GDP) of 1301.79. However, a large portion of India’s freshwater has not been considered yet, and there is a need to account for precise regional carbon budgets. Therefore, in this review, GHG emissions from India’s freshwater bodies, drivers behind GHG emissions (e.g., pH, mean depth, dissolved oxygen, and nutrients), and long-term climatic risks are thoroughly reviewed. Besides research gaps, future directions and mitigation measures are being suggested to provide useful insight into the carbon dynamics (sink/source) and control of GHG emissions.