The role of intertidal seaweeds in the primary production of mesotidal and macrotidal estuaries has been examined by means of a model, applied to the Tagus Estuary (Portugal). Special attention was paid to the description of the underwater light climate in intertidal areas, and to the importance of the formation of tidal pools. Two approaches were compared for the simulation of suspended particulate matter (SPM) in the pool areas, using three algal species. The use of an erosion–deposition approach to simulate the distribution of SPM in tidal pools gives an increase in net primary productivity per unit area of between 130 and 1300%, when compared to the more conventional approach where the suspended matter in the overlying water in intertidal areas is considered identical to that in the channels. The upscaled erosion–deposition model was applied to tidal pool areas and combined with the more conventional model for other intertidal areas. Results show that annual carbon fixation by intertidal seaweeds in the estuary exceeds 13,500 t C yr−1, and accounts for 21% of the total carbon fixed by all primary producers. The corresponding nitrogen removal by seaweeds corresponds to the annual nutrient loading of a population of 490,000 inhabitants.