Abstract: Seawater intrusion is the primary cause of groundwater salinisation in coastal aquifers. However, attributing salinisation solely to seawater intrusion may not always be accurate, given the likely presence of other sources. To understand if salinisation comes from seawater intrusion and its onset is crucial for groundwater management, but there are no definite threshold values for common indicators such as chlorides. Based on 1662 groundwater analyses from five Mediterranean coastal aquifers, the study aimed to distinguish the effects of mixing with present-day seawater from those caused by other sources. The trend analysis of cumulative probability plots of chloride (and total dissolved solids) is a key method for discriminating different groundwater salinisation sources and processes. Results establish that chloride, as a non-reactive tracer, is a more reliable indicator of seawater intrusion than total dissolved solids, a reactive indicator. A chloride concentration threshold of 200 mg/L identifies the seawater intrusion onset. The threshold validation comes from groundwater salinisation facies, as provided by groundwater-type codification. Fresh groundwater (Cl < 200 mg/L) anomalous total dissolved solids highlight the input of non-chloride salts and pollutants, providing caution regarding using total dissolved solids to recognise seawater intrusion. Beyond the threshold (Cl > 200 mg/L), data disclose emergent signals of salinisation sources and water–rock interaction processes overlapping seawater intrusion or the involvement of saline fluids different from present-day seawater. The threshold and a new categorisation of groundwater in coastal aquifers according to salinisation processes provide a benchmark for identifying and managing seawater intrusion in the Mediterranean area.