Direct measurement of methane emissions is cost-prohibitive for greenhouse gas offset projects, necessitating the development of alternative accounting methods such as proxies. Salinity is a useful proxy for tidal marsh CH₄ emissions when comparing across a wide range of salinity regimes but does not adequately explain variation in brackish and freshwater regimes, where variation in emissions is large. We sought to improve upon the salinity proxy in a marsh complex on Deal Island Peninsula, Maryland, USA by comparing emissions from four strata differing in hydrology and plant community composition. Mean CH₄ chamber-collected emissions measured as mg CH₄ m⁻² h⁻¹ ranked as S. alterniflora (1.2 ± 0.3) ≫ High-elevation J. roemerianus (0.4 ± 0.06) > Low-elevation J. roemerianus (0.3 ± 0.07) = S. patens (0.1 ± 0.01). Sulfate depletion generally reflected the same pattern with significantly greater depletion in the S. alterniflora stratum (61 ± 4%) than in the S. patens stratum (1 ± 9%) with the J. roemerianus strata falling in between. We attribute the high CH₄ emissions in the S. alterniflora stratum to sulfate depletion likely driven by limited connectivity to tidal waters. Low CH₄ emissions in the S. patens stratum are attributed to lower water levels, higher levels of ferric iron, and shallow rooting depth. Moderate CH₄ emissions from the J. roemerianus strata were likely due to plant traits that favor CH₄ oxidation over CH₄ production. Hydrology and plant community composition have significant potential as proxies to estimate CH₄ emissions at the site scale.