The transport of methane from sediments to the atmosphere by rising gas bubbles (ebullition) can be the dominant, yet highly variable emission pathway from shallow aquatic ecosystems. Ebullition fluxes have been reported to vary in space and time, as methane production, accumulation, and bubble release from the sediment matrix is affected by several physical and bio-geochemical processes acting at different timescales. Time-series analysis and empirical models have been used for investigating the temporal dynamics of ebullition and its controls. In this study, we analyzed the factors governing the temporal dynamics of ebullition and evaluated the application of empirical models to reproduce these dynamics across different timescales and across different aquatic systems. The analysis is based on continuous high frequency measurements of ebullition fluxes and environmental variables in a mesotrophic subtropical and polymictic freshwater reservoir. The synchronization of ebullition events across different monitoring sites, and the extent to which ebullition was correlated to environmental variables varied throughout the three years of observations and were affected by thermal stratification in the reservoir. Empirical models developed for other aquatic systems could reproduce a limited fraction of the variability in observed ebullition fluxes (R2 < 0.3), however the predictions could be improved by considering additional environmental variables. The model performance depended on the timescale. For daily and weekly time intervals, a generalized additive model could reproduce 70 and 96% of ebullition variability but could not resolve hourly flux variations (R2 = 0.19). Lastly, we discuss the potential application of empirical models for filling gaps in ebullition measurements and for reproducing the main temporal dynamics of the fluxes. The results provide crucial information for emission estimates, and for the development and implementation of strategies targeting at a reduction of methane emissions from inland waters., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Marcon et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)