Alterations of freshwater flow regimes and increasing eutrophication can lead to alterations in phytoplankton biomass, composition, and growth in estuaries and adjacent coastal waters. Since phytoplankton is the first trophic level of most aquatic foodwebs, these changes can be propagated to other biological compartments, eventually impacting water quality and ecosystem services. However, phytoplankton responses to environmental changes in abiotic variables (e.g., light, nutrients) are additionally controlled by mortality or removal processes (e.g., grazing, horizontal advection and viral lysis). Grazing exerted by microzooplankton, usually dominated by phagotrophic protists, is considered the most relevant phytoplankton mortality factor in most aquatic systems (see Calbet, Landry 2004). In fact, grazing impact of microzooplankton can prevent phytoplankton accumulation in marine systems despite an overall increase in phytoplankton replication rate. By consequence, microzooplankton grazing may minimize problems associated to increased eutrophication and, ultimately, prevent the occurrence of harmful phytoplankton blooms. Thus, microzooplankton grazing on phytoplankton constitutes a key biological process required to understand and predict relationships between hydrological and biological processes in aquatic ecosystems and to use ecosystem properties to improve water quality and enhance ecosystem services, general principles of the Ecohydrology Concept (Zalewski 2000).