Hydroelectric power reservoirs have been identified as potentially important sources of greenhouse gas (GHG) emissions due to the large areas of habitat which are inundated, leading to doubts as to whether hydropower is actually a net low-carbon energy source. In this study we propose a ‘service-to-service’ ecological analysis of inundated habitats from the viewpoint of carbon stock balance compared with the carbon stock loss from hydropower reservoirs. We consider whether the lost ecological service of carbon sequestration by inundated farmland, grassland and woodland could be offset by an increased ecological service provided by a grassland rehabilitation project. We also establish an integrated ecological compensation accounting methodology for inundated habitats by combining habitat equivalency analysis and estimates of carbon stock loss. This ecological compensation framework is illustrated by calculations from a case study of the Pondo hydropower project in Tibet, China. The results estimate that the total carbon stock losses from the construction and operation of this reservoir was 124,662 tons; requiring a compensatory restoration of areas of slightly, moderately, or severely degraded grasslands of 17.80, 8.90, and 5.93 thousand hectares, in a lump-sum payment mode. By means of such ecological compensations, carbon stock balance could be realized at the watershed scale, and the advantages of low-carbon hydropower developments could be fully realized.