Freshwater reservoirs are a globally significant source of atmospheric methane, contributing an estimated 6% of anthropogenic methane emissions. However, substantial uncertainty remains in reservoir methane budgets, limiting confidence in emission estimates from local to global scales. This uncertainty arises from limited data availability in key regions, particularly the Southern Hemisphere, and from the spatially heterogeneous nature of methane emission pathways. Bubble emissions and diffusive fluxes represent the two primary pathways, yet bubble emissions can exceed diffusive fluxes by several orders of magnitude and are often concentrated within small areas of reservoirs. Understanding the environmental drivers of these fine-scale processes is therefore critical for improving large-scale greenhouse gas assessments. Here, we synthesise findings from a 15-year research program investigating methane emissions across 16 freshwater reservoirs spanning subtropical South East Queensland and temperate Tasmania. We quantified the relative importance of diffusive and bubble-mediated methane fluxes and examined the environmental factors controlling spatial and temporal variability in emissions. Bubble emissions were highly variable among reservoirs, contributing between 10% and more than 90% of total methane emissions, and represented the dominant emission pathway in 12 of the 16 reservoirs studied. Detailed field investigations identified reservoir drawdown, changes in atmospheric pressure, and catchment-derived organic matter loading as key drivers of bubble emissions. By linking local-scale biogeochemical and hydrological processes to whole-reservoir methane budgets, this work demonstrates how mechanistic understanding of small-scale emission dynamics can substantially improve regional and global greenhouse gas estimates. We present a scalable empirical framework for spatially weighting methane emission pathways and reducing uncertainty in reservoir emission inventories. These findings provide a pathway for improving greenhouse gas accounting and are relevant to researchers, water managers, industry and government agencies seeking robust methods for quantifying reservoir emissions under a changing climate.