Estuaries are biogeochemical reactors able to modulate the transfer of energy and matter from the watershed to the coastal zones and to retain or remove large amounts of terrestrially generated nutrients. However, they may switch from nutrient sink to source depending upon interannual variability of the nutrient supply and internal processes driving whole system metabolism (e.g., net autotrophic or heterotrophic). We tested this hypothesis in the Curonian Lagoon, a hypertrophic estuary located in the south east Baltic Sea, following the budget approach developed in the Land-Ocean Interactions in the Coastal Zone (LOICZ) project. Annual budgets for nitrogen (N), phosphorus (P), and silica (Si) were calculated for the 2013–2015 period. The lagoon was divided in a flushed, nutrient loaded area, and in a confined, less loaded area. The lagoon was always a sink for dissolved inorganic Si and P whereas it was a N sink in the confined area, dominated by denitrification, and a N source in the flushed area, due to dinitrogen (N₂) fixation. The net ecosystem metabolism (NEM) indicated that the Curonian Lagoon was mainly autotrophic because of high primary production rates. In this turbid system, low N:P ratio, high summer temperatures, and calm weather conditions support high production of N₂-fixing cyanobacteria, suppressing the estuarine N-sink role.

Coastal lagoons are threatened by natural and anthropogenic factors that have been accelerated in the last decades, with detrimental effects on ecosystem and water quality, especially in sheltered systems. Eutrophication, macroalgal blooms, hypoxia and anoxia are among the main threats, which also impact on human activities, e.g. aquaculture and fishery. Study were performed from late 1980s to date in several Mediterranean lagoons, mainly in the Po river delta, in order to elucidate the main causes of such degenerative processes. Here we review (1) relationships between benthic vegetation and sediment biogeochemistry, with focus on factors determining eutrophication; (2) development of macroalgal blooms, with focus on causes and biogeochemical triggers of bloom onset; (3) perturbation of nitrogen cycling due to changes in benthic vegetation assemblages; (4) relationships between primary producers and benthic fauna, especially farmed species; (5) possible feedback loops among shellfish and primary producers.

Coastal lagoon types of Western Greece were allocated to a spectrum of meso to polyhaline chocked lagoons; poly to euhaline restricted lagoons; and euhaline restricted lagoons along the Ionian Sea coast. This diversity comprises wide ranges of physical, chemical and environmental parameters in a seasonal and annual scale, which explains the variability in the distribution of benthic macrophytes. Four different macrophyte assemblages were distinguished, characterized by annual or perennial species. Extensive statistical analysis showed that salinity and nitrate concentrations had a great impact on the composition and distribution of macrophyte assemblages into lagoon types that also changed their abundance on a seasonal and annual scale. During the monitoring period, an important salinity shift in a chocked lagoon might cause the gradual loss of Zostera noltii and its replacement by Ruppia cirrhosa. Restricted lagoons were characterized by higher species diversity, while the other three identified macrophyte assemblages were dominated by the angiosperms Ruppia cirrhosa and Cymodocea nodosa. This integrated study of coastal lagoons is likely to be broadly applicable, since it was based on important parameters affecting such ecosystems, and the provided links between macrophyte assemblages and abiotic factors are of critical importance to improve management and environmental policies.

Eutrophication represents one of the most impacting threats for the ecological status and related ecosystem services of transitional waters; hence, its assessment plays a key role in the management of these ecosystems. A new multi-index method for eutrophication assessment, based on the ecological index MaQI (Macrophyte Quality Index), the trophic index TWQI (Transitional Water Quality Index), and physicochemical quality elements (sensu Dir. 2000/60/EC), was developed including both driver and impact indicators. The study presents a large-scale implementation of the method, which included more than 100 Italian lagoon sites, covering a wide variability of lagoon typologies and conditions. Overall, 35% of sites resulted in eutrophic status, 45% in mesotrophic, and 25% in oligotrophic status.