Saltwater intrusion (SWI) into coastal aquifer systems is a global threat along the coastal areas worldwide. Melioration infrastructure and implementation in the Neretva River delta in south-eastern Croatia lowered the groundwater level by 1.50–2.50 m beneath the mean sea level, creating preconditions for active SWI. River Neretva hydrological regime can be separated into rain and dry seasons. Contrary to rain season, dry season has been considered as critical for SWI. Exceedance of hydrological droughts with a duration of 6-8 months annually enables the intrusion of the seawater along the river Neretva upstream thus creating a boundary condition for SWI since the coastal aquifer is significantly fed by saltwater from riverbed. Climate changes additionally contribute to salinization of the area, primary through the increase of mean sea level and additional reduction in river discharge due to the precipitation absence. In this study, in-situ measurements in Opuzen, Komin and Metković (temperature (T), electrical conductivity (EC) and salinity (S)) are combined with continuous observations of the Adriatic Sea level and Neretva surface water elevation EC and T. By using Discrete Fourier Transform with t_tide harmonic analysis, coherence analysis and the Welch method, the tidal propagation along the estuary has been investigated as well as related salinity changes during dry period to define interdependences and time lags of observed variables. A one-dimensional (1D) advection–diffusion based analytical model has been applied to demonstrate how river discharge, tidal excursion, sea level fluctuations and the geometry of the estuary determine the salinity regime. Hereby, mean sea level and freshwater discharge have been identified as a main driving forces controlling the saltwater intrusion along the Neretva riverbed. 2D laboratory flume experiments have been used to mimic climate changes impact to aquifer salinization from the river Neretva primary through the mean sea level change.