A large set of biogeochemical (nutrients, dissolved and particulate organic matter), phytoplanktonic (biomass and photosynthetic activity) and bacterial (bacterial diversity and ectoenzymatic activities) parameters were determined to understand how the severe drought period relative to the 2009–2010 El Niño Modoki episode influenced biogeochemical cycling and phyto- and bacterio-plankton communities in Terminos Lagoon (Mexico) potentially prefiguring future environmental conditions due to expected trends in climate change. During the study period, the water column of Terminos Lagoon functioned globally as a sink, and especially as a "nitrogen assimilator", because of high production of particulate and dissolved organic matter although exportation of autochthonous matter to the Gulf of Mexico was weak. Coupling between top-down and bottom-up controls accounted for the diverse responses in phytoplankton productivity. Nitrogen and phosphorus stoichiometry mostly accounted for the heterogeneity in phytoplankton and bacteria distribution in the lagoon. In the Eastern part, we found a clear decoupling between areas enriched in dissolved inorganic nitrogen in the North close to Puerto real coastal inlet and areas enriched in phosphate (PO4) in the South close to 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) close to the river mouth. In the Western part of the lagoon, maximal phytoplankton development resulted from the coupling between Palizada river inputs of nitrate (NO3) and particulate organic phosphorus -PP- (but depleted in PO4) and bacterial activity transforming PP and dissolved organic phosphorus (DOP) to available PO4. The Chumpan River only marginally contributed to PO4 inputs due to its very low contribution to overall river inputs. 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 polycyclic aromatic hydrocarbon (PAH)-degraders, which are of significance in this important oil production zone.