The photosynthetic performance of coastal marshes, an important blue carbon ecosystem, under tidal flooding has not been studied extensively. Our study aimed to understand coastal marsh plant photosynthesis at different stages of tidal inundation. Our study answered a few fundamental questions related to the differences in the photosynthesis rates between air-exposed and submerged parts of the canopy. We studied marsh Photosystem II (PSII) operating efficiency (φPSII) through a fundamental vegetation property called the chlorophyll fluorescence (ChlF) through, which can reflect the efficiency of marsh plants to utilize absorbed light energy to carry out photosynthesis. We designed and deployed a novel field measuring system that that measures high temporal resolution ChlF and φPSII at leaf scale. Our field observations demonstrated the within canopy variation of Spartina alterniflora ChlF and φPSII across a range of tidal cycles and differing tidal amplitudes. We also observed greatly reduced but active underwater photosynthesis activities in fully submerged leaves, suggesting that S. alterniflora potentially remains a carbon sink during tidal inundation. We further developed an integrated approach for parameterizing φPSII with a set of high-resolution environmental and biophysical measurements, including air temperature (Tair), soil temperature (Tsoil), photosynthetically active radiation (PAR), tide height relative to the soil surface (WT), cloudiness index (CI), and the near-infrared reflectance of vegetation (NIRv). We incorporated these key meteorological and biophysical parameters into a random forest regression model to predict φPSII, which produced accurate results with a root mean square error of 0.9 (the observed φPSII ranges between 0.22 to 0.75). We also found that predicted S. alterniflora φPSII was predominantly driven by PAR, NIRv, Tsoil and WT. Our findings suggest that characteristics of salt marsh photosynthetic efficiency can be modelled by physiological and environmental variables. Our modeling revealed the seasonal and spatial variability of predicted φPSII over the Georgia Coastal Ecosystems Long Term Ecological Research (GCE-LTER) flux tower footprint. These findings will be beneficial in estimating salt marsh gross primary production (GPP). This novel framework can also be used as an important validation of ecosystem productivity models that rely on satellite data to study top of the canopy productivity.