The 2009–2010 period was marked by an episode of intense drought known as the El Niño Modoki event. Sampling of the Términos Lagoon (Mexico) was carried out in November 2009 in order to understand the influence of these particular environmental conditions on organic matter fluxes within the lagoon's pelagic ecosystem and, more specifically, on the relationship between phyto- and bacterioplankton communities. The measurements presented here concern biogeochemical parameters (nutrients, dissolved and particulate organic matter [POM], and dissolved polycyclic aromatic hydrocarbons [PAHs]), phytoplankton (biomass and photosynthesis), and bacteria (diversity and abundance, including PAH degradation bacteria and ectoenzymatic activities). During the studied period, the water column of the Términos Lagoon functioned globally as a sink and, more precisely, as a "nitrogen assimilator". This was due to the high production of particulate and dissolved organic matter (DOM), even though exportation of autochthonous matter to the Gulf of Mexico was weak. We found that "bottom-up" control accounted for a large portion of the variability of phytoplankton productivity. Nitrogen and phosphorus stoichiometry mostly accounted for the heterogeneity in phytoplankton and free-living prokaryote distribution in the lagoon. In the eastern part, we found a clear decoupling between areas enriched in dissolved inorganic nitrogen near the Puerto Real coastal inlet and areas enriched in phosphate (PO4) near the Candelaria estuary. Such a decoupling limited the potential for primary production, resulting in an accumulation of dissolved organic carbon and nitrogen (DOC and DON, respectively) near the river mouths. In the western part of the lagoon, maximal phytoplankton development resulted from bacterial activity transforming particulate organic phosphorus (PP) and dissolved organic phosphorus (DOP) to available PO4 and the coupling between Palizada River inputs of nitrate (NO3) and PP. The Chumpan River contributed only marginally to PO4 inputs due to its very low contribution to overall river inputs. The highest dissolved total PAH concentrations were measured in the El Carmen Inlet, suggesting that the anthropogenic pollution of the zone is probably related to the oil-platform exploitation activities in the shallow waters of the southern of the Gulf of Mexico. We also found that a complex array of biogeochemical and phytoplanktonic parameters were the driving force behind the geographical distribution of bacterial community structure and activities. Finally, we showed that nutrients brought by the Palizada River supported an abundant bacterial community of PAH degraders, which are of significance in this important oil-production zone.

The wide range of ecological goods and services provided by tropical coastal lagoons and wetlands are under considerable pressure due to the synergistic effects of local anthropogenic impact and global climate change. In transitional waters, salinity is a key driver of ecological processes mostly depending on the balance between marine and river inputs, a balance that can be significantly modified by climate change and by anthropogenic alteration of the watershed. Mesoamerica being considered as a climate change hot-spot and as an ecoregion strongly vulnerable to global change, our study aimed at analyzing the relationship between salinity, river runoff, and rainfall variability in a tropical coastal lagoon and to assess the respective influence of climate change and watershed management. The study focusing on the large and shallow coastal lagoon of Laguna de Terminos in south eastern Mexico established: (1) the variability in salinity distribution along the yearly cycle and the occurrence of a high salinity anomaly period during the wet season of 2009; (2) the relationship between lagoon waters salinity and river inputs further underlying the anomalous situation encountered in 2009; (3) a long term increase in river discharge during the past 60 years, indicating potential salinity decrease in the lagoon during that same period; (4) an absence of any change in rainfall linking the increase in runoff to watershed management rather than long term trend in climate change. Additionally, the specific context of the 2009–2010 Central-Equatorial Pacific El Niño is underlined and the potential relationship between river discharge and ENSO is discussed. Those results should be of significant practical value to decision-makers who are often keen to point the finger at global climate change when local environmental management is also and sometime most significantly responsible.

The French archipelago of New Caledonia hosts one of the three most extensive reef systems in the world and was partly added to the UNESCO World Heritage List in 2008. In the very specific context of rapidly growing land-based mining extraction and ore processing activities, industrial managers, political decision makers, lagoon users and citizens have been expressing an increasing demand for the implementation of efficient environmental monitoring programs dedicated to the effects related to mining activities. As a result, New Caledonia lagoons were thoroughly studied particularly during the last two decades through national research projects. This chapter aims at reviewing the state-of-the-art of knowledge about the general features of New Caledonia geography and climatology, lagoon environmental drivers including hydrodynamics, pelagic and benthic processes, and the potential stress of terrestrial and anthropogenic inputs on marine communities. Insights addressing economic, ecological and political issues related to the complex status of self-governed New Caledonia are discussed with respect to living resources and environmental management.

Since 2005, wind-driven 'sporadic' coastal upwelling events have been identified off the southwestern reef of New Caledonia. Several studies have described the main physical processes and induced surface patterns using 1D and 3D modelling, as well as in situ measurements. Previous models were applied at the mesoscale without taking into account the lagoon. Using a recently developed 3D coupled physical-biogeochemical model that considers the complex ocean-lagoon interface, we aim to understand better the impact of the upwelling on the lagoon. The model was found to be in good agreement with measured data reported in previous publications about two upwelling events. However, in general, levels of surface chlorophyll-a were overestimated by the model in the upwelling area when compared to ocean colour data and several hypotheses have been proposed to explain the discrepancy. We then tracked rich upwelled water using a forward Lagrangian transport analysis. Upwelled waters from the upper nutricline were found to be able to reach the South West lagoon. An anti-cyclonic eddy was detected near the upwelling area, potentially responsible, in part, for the rich water intrusions into the lagoon.