Saltwater intrusion along rivers is a complex process controlled by multiple factors and thus fluctuates with a highly nonlinear nature and time-varying characteristics. It is challenging to monitor saltwater intrusion. The objective of this study was to clarify the spatial-temporal variation of saltwater intrusion and its potential impact on agriculture in the Po River Delta (Italy). 2006 was the most severe year of saltwater intrusion in the period we considered. 2022 was even worse, but the data are still under processing. In this study, the Hilbert-Huang transform (HHT) and rescaled range (R/S) were used to identify the multi-time scales and change trends of the salinity and discharge in 2006. After that, the time-dependent intrinsic correlation (TDIC) was used to depict intrinsic relationships between salinity and discharge at different time scales. The results showed that discharge and salinity exhibited behaviours of positive long-range correlation during different periods. The temporal series of salinity and discharge was decomposed into six intrinsic mode functions (IMF) and residuals based on the ensemble empirical mode decomposition (EEMD). The sum of variance contribution rates of IMF1 (4 days), IMF2 (10 days), and IMF3 (12.1 days) of salinity was more than 75%. All measured TDICs have highlighted strong correlations between salinity and discharge. Furthermore, we used spatial interpolation techniques to map salinity data along rivers. This allowed the investigation of dynamic changes in saltwater intrusion patterns during periods of severe drought. Outcomes show a significant negative correlation between salinity and normalized difference vegetation index (NDVI), indicating that the study area's agricultural greening was affected by saltwater intrusion.