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Photosynthetic microphytobenthic activity has increasingly been examined using pulse-amplitude-modulated (PAM) fluorescence techniques. Nevertheless, estimating carbon production rates from fluorescence measurements implies the establishment of reliable relationships. The aim of this study was to determine such a relationship from field measurements of both PAM fluorescence and CO2 fluxes. Three study sites of varying sedimentary features were investigated in different seasons. Both linear and with plateau relationships were obtained between the fluorescence parameter (relative electron transport rate [rETR]) and the community-level carbon-fixation rate (gross community primary production rate [GCP] in mg C · m−2 · h−1). The correlation calculated from the whole data set (i.e., all sites and all seasons) was very strong (n = 106; r = 0.928). Significant correlations were also obtained for light-curve parameters assessed with the two methods: Pm (n = 8; r = 0.920) and Ik (n = 8; r = 0.818). Total community-level carbon fixation for the emersion period was calculated from fluorescence measurements according to the relationship established between GCP and rETR, and between light-curve parameters, and the results were compared to the estimation obtained directly from GCP measurements. The agreement between the two estimations was quite good for both ways of calculation (with a mean discrepancy of 30% for the first one and −2% for the second one). These results suggest the potential application of PAM measurements to calculate carbon-fixation rates at large spatial and temporal scales, provided that a set of experiments coupled with CO2-flux measurements are performed.