Primary production of the microphytobenthic community and carbohydrates concentrations were studied in the lagoonal system of Grado and Marano, located in the Northern Adriatic coast. Sediment samples were collected along a salinity gradient. Abundance and species composition of the microphytobenthic communities were analysed and the benthic microalgal biomass was estimated as Chlorophyll a (Chl a). Primary production of benthic diatoms was estimated using C-14-tracer. Extracellular carbohydrates were extracted from the sediment and separated in two operationally defined fractions (colloidal and EDTA-extractable). Salinity was higher in the Grado lagoon, where the benthic microalgal community was mainly composed of marine diatoms. In the Marano lagoon, which has a lower salinity, freshwater species were also found. In both lagoons, photosynthetic efficiency showed an inverse relationship with salinity and a direct relationship with the main biological variables. Photosynthetic activity was directly related to Chl a and abundance of benthic microalgae, suggesting that in the benthic system microalgal community is responsible for primary production. Overall, salinity was also influent on the microphytobenthic primary production, which was greater in the more saline Grado lagoon.