<p>Salinity is considered one of the key parameters controlling estuarine ecosystem functioning and biota distribution. This study proposes a novel mapping approach to identify dominant ecological salinity zones along an estuarine water body and obtain a statistical-based view of changes in salinity patterns caused by alterations in freshwater input. Salinity Zones Distribution (SZD) maps provide an objective analysis tool to improve environmental management of estuarine biota in diverse scenarios of salinity alteration such as freshwater regulation or sea-level rise for instance. In this study, we simulated the salinity hydrodynamics for a major estuary in Brazil, where a dam regulates the freshwater inflow near the estuary head. The application of the SZD mapping for the Paraguaçu River shows the differences in ecological salinity zonation along the estuary for natural and regulated freshwater inflow. This mapping technique can be applied to estuaries all over the world and allows us to identify the possible groups of organisms associated with different salinity environments, providing alternatives for better management and sustainable use of natural resources.</p>