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The river-delta system of the Neretva, located in the southeastern Adriatic Sea, confronts the simultaneous influence of basin-driven processes and coastal oceanographic conditions, which together exert dominant control over the land-sea interaction and the balance between surface-water and groundwater regimes across the delta. River Neretva Delta represents the largest cultivated agricultural area (4500 ha) along the Croatian coast and it is increasingly exposed to climate change and reduced freshwater availability, which intensifies salinization through saltwater intrusion. Since the 1960s, the delta area has been significantly transformed from its natural state into an intensively cultivated landscape, primarily via the extensive implementation of melioration infrastructure. Up to date, after the preconditions for agriculture have been met, no significant improvements to the melioration system’s operating regime have been implemented, nor has novel infrastructure been introduced, although a clear decline in both freshwater quality and quantity is evident.This study aims to highlight the adverse effects of climate change, relying on datasets obtained via several cross-border collaboration programmes. Initially, monitoring was focused on capturing groundwater salinity and related volumetric features in the area. As an add-on, a monitoring infrastructure has been implemented to ensure insight into surface-water quality and quantity parameters. Since the Neretva River has been identified as a dominant boundary condition for the hydrological and hydrogeological setting of the delta, the estimation of the freshwater discharge has been significantly improved to ensure the real-time information on freshwater availability and on upstream penetration of the seawater wedge, which can infiltrate through the riverbed and feed the aquifer with saltwater. In addition to the onshore monitoring network, further activities led to the installation of subsea piezometers to support offshore groundwater characterization, sampling, and the collection of Rn222/226 datasets.Results obtained revealed several emerging trends. With ongoing sea-level rise, the impact of saltwater intrusion on freshwater availability is evident at both seasonal and short-term timescales. Land subsidence analyses highlight a steady trend with minor spatial variability. Upstream freshwater discharge is regulated by hydropower plants in operation, thereby reducing freshwater availability during the dry season. Even though the phreatic aquifer is sensitive to external conditions, deeper lithological units appear comparatively insensitive, reflecting the dominant influence of the Adriatic Sea and a persistent lack of freshwater throughout the hydrological year. Considering climate change-induced effects, this study indicates a deterioration of the water quality and highlights the associated challenges for water management.Research funded by the Interreg Italy–Croatia 2021–2027 Programme, Project ID: ITHR0200479—SWAMrisk “Subsurface Water Monitoring and Management to Prevent Drought Risk in Coastal Systems”.