Doñana National Park is located in the southwest of the Iberian Peninsula, where water scarcity is recurrent, together with a high heterogeneity in species and ecosystems. Monitoring carbon assimilation is essential to improve knowledge of global change in natural vegetation cover. In this work, a light use efficiency (LUE) model was applied to estimate gross primary production (GPP) in two ecosystems of Doñana, xeric shrub (drought resistant) and seasonal marsh (with grasslands dependent on water hydroperiod) and validated with in situ data from eddy covariance (EC) towers installed in both ecosystems. The model was applied in two ways: (1) using the fraction of absorbed photosynthetically active radiation (FAPAR) from Sentinel-2 and meteorological data from reanalysis (ERA5), and (2) using Sentinel-2 FAPAR, reanalysis solar radiation (ERA5) and the Sentinel-2 land surface water index (LSWI). In both cases and for both ecosystems, the error values are acceptable (below 1 gC/m2) and in both ecosystems the model using the LSWI gave better results (R2 of 0.8 in marshes and 0.51 in xeric shrubs). The results also show a greater influence of the water status of the system than of the meteorological variables in this area.