One of the areas of prior interest for the Republic of Croatia in terms of water conservation and water needs, especially for irrigation of agricultural crops, is the river Neretva delta. This area represents the largest agricultural area on the Croatian coast and is the source of existence for the local population. Managing the area has become a complex task given the intensive agricultural activities, the large number of people living near the area of interest, significant seawater intrusion (SWI) and ongoing climate changes manifested by indicators such as sea level rise and increasingly unpredictable precipitation. Therefore, the need to understand the processes responsible for creating favorable/unfavorable conditions in both, surface and groundwater, is self-evident. A review of the available literature reveals that SWI in the coastal aquifer system of the Neretva Valley, with a focus on external loadings and their effect on ground and surface water has not been sufficiently investigated. The influence of the operative regime of the melioration system, the hydrological regime of the river Neretva and the tidal characteristics of the Adriatic Sea to ground and surface water fluctuations along the study area was established as the primary scope of this thesis. A variety of methodological approaches was used throughout the thesis to analyze and investigate the impact of SWI on the Neretva coastal aquifer system. Despite the strong effect of the SWI, the area of interest is defined as a complex system that can be controlled naturally or by management. In order to investigate the interaction between factors controlling the surface and ground water along the Neretva Valley in conjunction with SWI, a monitoring system was designed and implemented to collect pertinent data sets and time series. An investigation was conducted utilizing time series in the temporal and frequency domains. The application of cross correlation methods, the Discrete Fourier Transform and the Continuous Wavelet Transform provided insights into the interdependence of analyzed ground and surface water parameters. Based on past in-situ work and time series of sea water elevation and piezometric head, the study area was hydrogeologically characterized. Previously collected in-situ data were used for the conceptualization of the coastal aquifer system. Tidal methods were upgraded to incorporate tidal signals with more than one harmonic constituent to improve the method’s capacity. Findings are focused on determining specific storage, hydraulic conductivity and leakance between shallow unconfined and deeper confined aquifer units. Novel in-situ and laboratory results were utilized to bolster these findings. The confinement of the deeper aquifer was confirmed in two ways: i) by using frequency analysis of constituents typical for confined conditions which confirm confinement of deeper aquifer and ii) by using ERT results which do not evidence the absence of confining clay layer along the study area. The determined values of hydraulic conductivity were consistent with the gravely material, which was confirmed by interpreting the characteristic grain values determined in the laboratory from borehole cores taken from the study area. Based on the hydrogeological characterization and determination of the connectivity between the geological units of the aquifer, the predominant SWI corridors characterizing rain and dry seasons were identified. To comprehend the transient nature of surface and groundwater parameters such as temperature, piezometric head, and electrical conductivity, a number of external loadings were considered. The confined aquifer appears to maintain its electrical conductivity regime independently from the unconfined aquifer above and vice versa. The electrical conductivity in the confined aquifer shows no significant correlation with tidally-induced oscillations, while piezometric head as observed within the confined aquifer is shown to be driven by tidal oscillations. In addition to the confined aquifer, it was demonstrated that the Adriatic Sea is the dominant factor controlling the groundwater regime in the Diga area, as found in the unconfined aquifer. The melioration system’s operative regime creates favorable agricultural conditions in the study area. As a result, groundwater has been delineated below sea levels, thereby creating active SWI conditions that increase the inflow of seawater from the Adriatic Sea. The majority of precipitation occurs during the rain season, which creates an imbalance in the natural aquifer recharge. In both rain and dry seasons, the river Neretva's hydrological regime plays a dominant role but with opposite effects. During the dry season, seawater intrudes upstream along the Neretva riverbed, generating a source of seawater that impacts the Jasenska region. Specific attention has been given to the sub melioration systems of Vidrice and Opuzen ušće. The groundwater of the coastal area of Opuzen ušće, called Diga, was identified as dominantly tide controlled, while the Vidrice area is predominantly influenced by the presence of upstream springs of brackish water which enter the melioration system. It was discovered that only the Vidrice area has higher salinity during the rain season than during the dry season. The operative regime of the melioration system controls the dynamics of water quality as found along the Vidrice area, while the groundwater in the Jasenska area is salinized primarily by the Neretva River.