Groundwater in coastal aquifers of Mediterranean regions plays an essential role in sustaining ecosystems and human activities. Their geographical position and geomorphological characteristics make them often vulnerable to hydro-climatic hazards, such as seawater intrusion, groundwater depletion and pollution, which are related to frequent and intense drought events, rising temperatures, intensive groundwater exploitation, and use of fertilisers. To this end, the spatial and temporal evolution of groundwater salinization and nitrate pollution in the coastal karst aquifer of Salento, southern Italy, was investigated using multivariate statistical methods (Hierarchical Cluster Analysis and Factor Analysis) and hydrogeochemical techniques (Hydrogeochemical Facies Evolution) to classify groundwater samples and identify the main pollution processes. Additionally, Indicator Kriging was used to analyse nitrate pollution trends over a 25-year period. Results of these techniques applied for the Salento aquifer allowed the delineation of the main ongoing processes, i.e. groundwater salinisation and nitrate pollution, identifying the areas most affected. The salinisation process intensifies at the end of dry periods, where the lack of rainfall and the increase in water demand for irrigation purposes lead to more significant withdrawals from wells. Nitrate pollution, conversely, is not correlated with the use of nitrogen-based fertilisers or changes in land use, showing how the system’s response to mitigation practices is delayed in time. In the absence of systematic sampling, it is not possible to establish with certainty whether current concentrations have surpassed the peak related to the massive use of nitrogen fertilisers in the past. Statistical methods are suitable for identifying ongoing processes where continuous monitoring data records are absent. Finally, the results of the different techniques are superimposed, corroborating their effectiveness. Findings demonstrate the necessity of long-term monitoring and strategic water resource management to prevent further deterioration of water quality in vulnerable karst aquifers.