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Mangroves are complex ecosystems subject to periodic and irregular changes in meteorology, tides, water quality and biological factors. Methane dynamics in mangroves and their dependence on biogeochemical controls across scales are poorly characterized using traditional parametric statistics. We measured the ecosystem‐scale methane flux (F_CH4) using an eddy covariance system in a subtropical estuarine mangrove for two years. A combination of nonparametric statistical approaches, including singular spectrum analysis and information theory, was used to isolate multiscale F_CH4 variations and explore their variability and dominant controls at different time scales. F_CH4 exhibited the largest variability at the diel scale (57%), followed by seasonal (25%) and multiday (18%) scales. Mutual information metrics suggested that variation in F_CH4 was dominantly coupled to plant activities through synchronous …