Hydropower is a reliable source of renewable energy that can support the low-carbon energy transition, even though man-made reservoirs can be significant sources of greenhouse gas (GHG) emissions. A multitude of studies have been undertaken to examine the temporal and spatial patterns of GHG emissions from reservoirs, yet no thorough examination of the influence of reservoir hydrological conditions on these emissions has been made. In this study, GHG emissions from hydroelectric reservoirs with varying volumes of water, hydraulic retention times, and power densities were evaluated for a 100-year timescale. GHG emissions from hydropower generation over a 100-year period were significantly lower than those from thermal power generation. Notably, the post-impoundment emission rates averaged 4.27 g CO2 equivalents (CO2eq)/m2 per day, with a net rate of 3.17 g CO2eq/m2 per day. The average post-impoundment emission per unit of electricity generated was 17.22 g CO2eq/kWh, which was lower than the global average of 273 g CO2eq/kWh. Moreover, the emission rates were negatively correlated with volume (post-impoundment, r = – 0.70, p < 0.001; net, r = – 0.33, p = 0.06) and hydraulic retention time (post-impoundment, r = – 0.97, p < 0.001; net, r = – 0.46, p < 0.01). The post-impoundment (r = – 0.81, p < 0.001) and net (r = – 0.62, p < 0.001) emissions per unit of electricity produced exhibited a negative correlation with power density. Reservoirs with higher power densities, shorter hydraulic retention times and smaller capacities were demonstrated to have considerable advantages and potential for the mitigation of GHG emissions due to the their lower emissions of GHG per unit of electricity generated.