Despite large carbon pools in intertidal mudflats, carbon cycling and fluxes are poorly constrained, and this creates major gaps in the Blue Carbon literature. Microphytobenthos (MPB) are thought to be the dominant pathway regulating sediment-atmosphere CO2 flux through their combined uptake and respiratory emission. Little is known about the variability of uptake and emission across seasons. We present the quantification of vertical flux of carbon between the MPB on the mudflat surface and the atmosphere in the upper Bay of Fundy, New Brunswick to better understand environmental drivers influencing photosynthetic uptake and respiration losses. CO2 flux on mudflat exposed to air was measured using benthic chambers alongside sediment temperature, Photosynthetically Active Radiation (PAR), and spectral index NDVI as a proxy of MPB’s biomass. Data were collected over three two-week sampling campaigns in spring, summer and fall 2025. Multilinear regression analysis explained PAR and temperature as the largest drivers of Net Ecosystem Exchange (slope: 0.004 µmol CO2 m-2 s-1/µmol photons m⁻² s⁻¹ and 0.06 µmol CO2 m-2 s-1 °C⁻¹ respectively), where Respiration was closely associated only with NDVI (slope = 0.79). Both NEE and Respiration showed suppression for the first hour after tidal emergence. Seasonal comparison explained higher uptake during summer, while fall season was characterized by lower photosynthetic activity. We found seasonal variability in CO2 fluxes was mainly governed by light availability, temperature, tidal exposure and MPB biomass.