During an annual cycle, overlying water and sediment cores were collected simultaneously at three sites (Tavira, Culatra and Ramalhete) of Ria Formosa's intertidal muddy and subtidal sandy sediments to determine ammonium, nitrates plus nitrites and phosphate. Organic carbon, nitrogen and phosphorus were also determined in superficial sediments. Ammonium and phosphate dissolved in porewater were positively correlated with temperature (P < 0.01) in muddy and sandy sediments, while the nitrogen-oxidized forms had a negative correlation (P < 0.02) in muddy sediments probably because mineralization and nitrification/denitrification processes vary seasonally. Porewater ammonium profiles evidenced a peak in the top-most muddy sediment (380 lM) suggesting higher mineralization rate when oxygen is more available, while maximum phosphate concentration (113 lM) occurred in the sub-oxic layer probably due to phosphorus desorption under reduced conditions. In organically poor subtidal sandy sediments, nutrient porewater concentrations were always lower than in intertidal muddy sediments, ranging annually from 20 lM to 100 lM for ammonium and from 0.05 lM to 16 lM for phosphate. Nutrient diffusive fluxes predicted by a mathematical model were higher during summer, in both muddy (104 nmol -2 ), while during lower temperature periods these fluxes were 3-4 times lower. Based on simulated nutrient effluxes, the estimated annual amount of ammonium and phosphate exported from intertidal areas was three times higher than that released from subtidal areas (22 ton year -1 --NH 4 + ; 2 ton year -1 --HPO 4 -2 ), emphasizing the importance of tidal flats to maintain the high productivity of the lagoon. Global warming scenarios simulated with the model, revealed that an increase in lagoon water temperature only produces significant variations (P < 0.05) for NH 291-304 DOI 10.1007/s10533-007-9076-4 will probably affect the system productivity due to a N/P ratio unbalance.