A seasonally pumped, multi-layered confined coastal aquifer in the Western Port Basin (southeast Australia), was assessed using environmental isotopes to identify the origins of salinity, to determine the hydrogeological and palaeo-environmental controls on salinity distribution at the coast, and to examine the effects of seasonal pumping on hydraulic response and salinity change in the aquifer. The spatial distribution of salinity was examined along an east-west transect along the coastline in conjunction with a range of geological, isotopic and chemical data, which allowed assessment of different salinity sources and emplacement mechanisms through time. The geology beneath the coastline consists of a series of water-bearing sedimentary (marine and terrestrial) and igneous Cainozoic formations, confined by a thick Quaternary swamp clay deposit. Two distinctive types of vertical salinity profile – decreasing and increasing salinity with depth – were observed at different locations along the coast, indicating that the typical situation of a dense saltwater wedge underlying fresh groundwater is an over-simplification. Chloride concentrations, stable water isotopes, and radiocarbon in groundwater indicate various degrees of mixing between pre-modern marine water and fresh meteoric groundwater. The complex geological structure and geomorphological history have resulted in a range of salinity distributions that are unlikely to be stable in the long term. Difference in the vertical salinity profiles are due to key factors which include: 1) aquifer thickness and permeability, 2) recharge rates/onshore aquifer pressures, 3) degree of confinement between aquifer units, and 4) influence of changing sea-levels since the Last Glacial Maximum and through the Holocene.<br><br>Molar Cl/Br ratios in groundwater range from 613 to 1003, indicating salts present in groundwater are of marine origin. The most saline samples resemble seawater in chemical composition (Na/Cl=0.79-0.84, TDS=36,020-40,537 mg/L, Mg/Cl=0.10-0.11, Cl/Br=681-706). However, stable isotopic values of some saline samples are lower than typical seawater (d18O=-2.4 to 0.1‰ & d2H=-22.1 to -0.8‰), and the saline groundwater have radiocarbon activities which are pre-modern (e.g. 28 to ~60 pMC) indicating emplacement at some time previously during the Holocene. The current relationship between sea-level and ground surface, along with the radiocarbon data appear to rule out modern seawater intrusion as an emplacement mechanism. The emplacement of this saline water, now preserved in the coastal sediments, occurred by surface inundation of the coastal sediments during the sea level maximum at c. 5-6kyr BP and/or possibly earlier, in the immediate post-glacial sea level rise event. Chloride and stable isotope relationships in the saline samples show that these samples are of seawater-like salinity, but have stable isotope values suggesting a marine component only 54.3 to 81.4%. Hence, these are 35.5 to 92% more saline than can be explained by conservative mixing of fresh and marine water, which could be explained by mineral dissolution, or transpiration and solute exclusion by halophytic vegetation. This study proposes a source water which started out as various mixtures of freshwater and seawater, probably the result of mixing in an estuarine-swamp environment, and/or mixing of marine water with pre-existing freshwater in the system; the major salinization mechanism is transpiration of estuarine water by halophytic vegetation (e.g. mangroves) and secondary processes such as evaporation and mineral dissolution (e.g. large amounts of carbonate and minor halite dissolution).<br><br>The difference in the existence and vertical distribution of this palaeo-seawater mixture in the aquifer around the coastline is a function of the geology – in some areas it remains trapped in the upper part of the aquifer system where low permeability clays confine the deeper permeable units; in others the saline water has propagated to deeper levels due to a lack of low permeability cover. Saline water trapped in low-permeability units at the coast is likely to be experiencing gradual top-down freshening from rainfall infiltration, and a slow downward release of salinity into more permeable underlying layers due to natural density driven flow and pumping of the confined aquifer.<br><br>The study determines the predominant hydrogeological controls on salinity distribution and salinization/freshening, proposing conceptual models to explain the different vertical distributions of groundwater salinity at the coastline. An improved understanding of the sources of salinity and the hydrogeological controls will subsequently provide support for the future management of groundwater in the Western Port Basin, and serve as a template for how to unravel complex salinity distributions in coastal aquifers, and their relationships to palaeo- and recent geomorphological histories.