Ria de Aveiro is a mesotidal coastal lagoon with one of the largest continuous salt marshes in Europe. The objective of this work was to assess C, N and P stocks of Spartina maritima (low marsh pioneer halophyte) and Juncus maritimus (representative of mid-high marsh halophytes) combined with the contribution of Halimione portulacoides, Sarcocornia perennis, and Bolbochenous maritimus to the lagoon ≈4400 ha marsh area. A multivariate analysis (PCO), taking into account environmental variables and the annual biomass and nutrient dynamics, showed that there are no clear seasonal or spatial differences within low or mid-high marshes, but clearly separates J. maritimus and S. maritima marshes. Calculations of C, N and P stocks in the biomass of the five most representative halophytes plus the respective rhizosediment (25 cm depth), and taking into account their relative coverage, represents 252053 Mg C, 38100 Mg N and 7563 Mg P. Over 90% of the stocks are found within mid-high marshes. This work shows the importance of this lagoon’s salt marshes on climate and nutrients regulation, and defines the current condition concerning the ‘blue carbon’ and nutrient stocks, as a basis for prospective future scenarios of salt marsh degradation or loss, namely under SLR context.