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The Neretva River is the largest river in the eastern part of the Adriatic basin with a total length of 218 km, of which only about 20 km are in Croatia. Saltwater intrusions into the Neretva River estuary have numerous negative impacts on agricultural production, freshwater resources, biodiversity and the balance of this fragile ecosystem. Therefore, understanding this phenomenon is important not only from scientific and ecological perspectives, but also for economic reasons. Unfortunately, the problem of salinization is expected to become even more severe in the future under projected climate change with rising sea level and decreased river discharge in summer. In this study, the dynamic nature of saltwater intrusions into the Neretva River estuary was analysed using long-term CTD (conductivity, temperature, and depth) measurements carried out monthly over a wide area of the estuary, as well as measurements conducted between March 2023 and 2024, but with higher spatial and temporal resolutions along the Croatian part of the Neretva River course. The long-term measurements were carried out at five marine CTD stations positioned in the close vicinity of the river mouth, while a sixth station was located within the Neretva River. Temperature and salinity profiles mainly influenced by heat and water air-sea fluxes and river discharge revealed seasonal changes in the spread of low-salinity river-influenced water. The recent high-resolution measurements included CTD profiles collected during six field cruises and continuous CTD, total oxygen, water pressure, water level, and meteorological measurements at selected locations along the watercourse. The CTD vertical profiles were collected at 13-19 quasi-evenly distributed stations from the river mouth to the town of Metković and revealed several characteristic patterns of the sea wedge’s intrusion. During the cold part of the year, with moderately high river discharge, saltwater intrusion was limited to the lower part of the estuary, spreading in the bottom layer over relatively short distances of up to 6 km from the river mouth. In contrast, summer conditions characterised by low river discharge allowed saltwater to spread over 20 km from the river mouth up to the town of Metković. An extreme event occurred in mid-May 2023 following a strong cyclonic disturbance accompanied by heavy rainfall. Detailed CTD measurements along the Neretva River course showed that low-salinity water occupied the entire water column, from the city of Metković to the river mouth. The strong Neretva River outflow (discharge of over 1400 m3/s) completely flushed the saltwater out of the river, resulting in near-homogeneous salinity profiles with values below 0.3. In addition to field cruises, autonomous CTD and total oxygen loggers were deployed at four locations along the course of the river, while meteorological and hydrological conditions were monitored by an automatic station located in the port of Metković. Overall, analysis of the collected data showed that saltwater intrusions are mainly influenced by river discharge, but also by weather conditions, tides, and human activities.