Coastal zones are dynamic and sensitive to changing forcing conditions related to climate variability, such as flooding and droughts, storm surges, and sea-level changes. Among coastal systems, deltas and estuaries are characterized by complex dynamics between fresh water of continental origin and salt waters (Horner-Devine et al., 2015; Valle-Levinson, 2010). Moreover, deltas are impacted by human activities and in some cases the anthropic control on the natural environment can override the climatic signal, forcing deltas toward a man-made river-dominated system (Maselli & Trincardi, 2013). One of the major problems affecting deltas and estuaries, especially during drought conditions, is the upstream extent of the mixing zone between freshwater and saltwater. This would lead to a consequent increase of the salt content in aquifers and surface waters. Saltwater intrusion (SWI) in rivers can hinder the use of surface water for irrigation or drinking purposes and can threaten the livelihood of coastal communities that rely on fresh water supplies for their livelihood. Furthermore, when there is contact between the channel bed and the underlying coastal aquifer, saltwater can intrude and lead to salinization of soils (Werner et al., 2013; White & Kaplan, 2017). A variety of factors drives SWI on different spatial and temporal scales. These can be natural (sea level, storm surges, hurricanes, climate fluctuations, and subsidence) or anthropogenic (land drainage, exploitation of coastal aquifers, reduction in freshwater discharge from hydropower production and irrigation, interbasin diversions and other hydraulic infrastructures, changes in land-use within the drainage basin and channel deepening), as well as combinations of both (White & Kaplan, 2017). Therefore, understanding the processes controlling SWI and their effects under climate change is crucial for defining proper coastal mitigation and management strategies.