Salt marshes are large carbon reservoirs as part of blue carbon ecosystems. Unfortunately, there is limited information about the net ecosystem (NEE) and methane (CH4) exchange between salt marshes and the atmosphere to fully understand their carbon dynamics. We tested the influence of biophysical drivers by plant phenological phases (i.e., Greenup, Maturity, Senescence and Dormancy) on NEE and CH4 exchange in a grass-dominated temperate tidal salt marsh. We used three years of data derived from eddy covariance, PhenoCam (to measure vegetation phenology), and ancillary meteorological and water/soil variables. Overall, NEE showed significant differences among all phenological phases (p 72% of the annual CO2 emissions in this ecosystem. Net CH4 emissions were higher during Maturity (3.7 g C-CH4 m2) and Senescence (4.2 g C-CH4 m2). Photosynthetically active radiation (PAR) substantially influenced (r2 > 0.57) daytime NEE across phenological phases, but a combination of variables including water table level (WTL), water temperature and atmospheric pressure were relevant to explain CH4 exchange. The study site was an overall net carbon source to the atmosphere with annual emissions of 13-201 g C-CO2 m−2yr−1 and 8.5-15.2 g C-CH4 m−2yr−1. Our findings provide insights on: a) the role of plant phenological phases on ecosystem-scale CO2 and CH4 fluxes; b) challenges for modeling ecosystem-scale CO2 and CH4 fluxes in salt marshes; and c) the potential net loss of carbon to the atmosphere that should be considered for carbon management and accounting in these ecosystems.