Coastal areas are characterized by considerable demographic pressure that generally leads to groundwater overexploitation. In the Mediterranean region, this situation is exacerbated by a recharge reduction enhanced by climate change. The consequence is water table drawdown that alters the freshwater/seawater interface facilitating seawater intrusion. However, the groundwater salinity may also be affected by other natural/anthropogenic sources. In this paper, water quality data gathered at 47 private and public wells in a coastal karst aquifer in Apulia (southern Italy), were interpreted by applying disparate methods to reveal the different sources of groundwater salinity. Chemical characterization, multivariate statistical analysis, and mixing calculations supplied the groundwater salinization degree. Characteristic ion ratios, strontium isotope (⁸⁷Sr/⁸⁶Sr), and pure mixing modelling identified the current seawater intrusion as a main salinity source, also highlighting the contribution of water–rock interaction to groundwater composition and excluding influence from Cretaceous paleo-seawater. Only the combined approach of all the methodologies allowed a clear identification of the main sources of salinization, excluding other less probable ones (e.g., paleo-seawater). The proposed approach enables effective investigation of processes governing salinity changes in coastal aquifers, to support more informed management.