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Abstract Methane dynamics within salt marshes are complex because vegetation types, temperature, oscillating water levels, and changes in salinity and redox conditions influence CH₄production, consumption, oxidation, and emissions. These non‐linear and complex interactions among variables affect the traditionally expected functional relationships and present challenges for interpreting and developing process‐based models. We employed empirical dynamic modeling (EDM) and convergent cross mapping (CCM) as a novel approach for characterizing seasonal/multiday and diurnal CH₄dynamics by inferring causal variables, lags, and interconnections among multiple biophysical variables within a temperate salt marsh using 5 years of eddy covariance data. EDM/CCM is a nonparametric approach capable of quantifying the coupling between variables while determining time scales where variable interactions are the most relevant. We found that gross primary productivity, tidal creek dissolved oxygen, and temperature were important for seasonal/multiday dynamics (rho = 0.73–0.80), while water level was most important for diurnal dynamics during both the growing and dormancy phenoperiods (rho = 0.72 and 0.56, respectively). Lags for the top‐ranked variables (i.e., gross primary productivity, dissolved oxygen, temperature, water level) occurred between 1 and 5 weeks at the seasonal scale and 1–24 hr at the diurnal scale. The EDM had high prediction capabilities for intra‐/inter‐seasonal patterns and annual CH₄sums but had limitations in representing large, infrequent fluxes. Results highlight the importance of non‐linearity, drivers, lag times, and interconnections among multiple biophysical variables that regulate CH₄fluxes in tidal wetlands. This research introduces a novel approach to examining CH₄fluxes, which will aid in evaluating current paradigms in wetlands and other ecosystems.