Coastal shallow lagoons are important ecosystems in terms of their high ecological relevance. They act as buffers of the land sea interface, providing valuable ecosystem services such as nutrient recycling, decomposition of organic matter and removal of pollutants. Lagoons are regions of restricted exchange, subject to anthropogenic pressures that result in problems such as eutrophication. Because they are shallow, submerged primary producers play a prominent role in lagoon system metabolism. Furthermore, coastal lagoons are particularly vulnerable to global climate change and may act as `sentinel systems'. Sea level rise already threatens to overwhelm some lagoons, such as Venice and Moroccan lagoons. Recent observations and studies have shown that a global climate change, especially the warming of the climate system and the sea level rise is unequivocal (IPCC, 2007). Therefore, the dCSTT-MPB model, which deals with nitrogen and chlorophyll concentrations in the water column and within the sediments, was used to explore a range of scenarios that aimed at representing these changes. The tendency of the light limitation due to the sea level rise is the potential degradation of the microphytobenthos community. This reduction would lead to stronger nitrogen fluxes from pore water to the water column, increasing significantly the nitrogen concentrations. No increase in the phytoplankton community was found because it is mainly influenced by the resuspension of microphytobenthos. High nitrogen concentration may be the first indication of an eutrophication event. Nonetheless, nitrogen may be exported to the sea and cause problems in the adjacent coastal waters. The increase in temperature did not lead to significant differences. (C) 2011 Elsevier Ltd. All rights reserved.