Abstract: In this study hydrochemical, isotopic and multivariate statistical tools are combined with a recharge analysis and existing geophysical data to improve understanding of major factors controlling freshwater occurrence and the origins of high salinities in the multi-layered coastal aquifer system of the Great Maputo area in Mozambique. Access to freshwater in this semi-arid area is limited by an inefficient public supply network, scarce surface waters, long droughts and an increasing population growth. Groundwater has a large potential to enhance water security, but its exploitation is threatened by both coastal and inland salinization mechanisms that are poorly understood. A GIS approach is utilized to classify potential recharge zones based on hydrogeological properties and land use/cover, whereas potential recharge rates are estimated through a root zone water balance method. In combination with water stable isotope data results reveal that extreme rainfall events provide the most relevant contributions to recharge, and interception and evaporation play an important role in the low recharge areas. Hierarchical clustering of hydrochemical and isotopic data allows the classification of six water groups, varying from fresh to brackish/salt waters. Corresponding scatter plots and PHREEQC modelling show evaporation and mixing with seawater (up to 5%) as major processes affecting salinity in the area. The co-occurrence of high alkalinity and Cl concentrations, in combination with piezometric and geo-electrical data, suggests that: 1) inland brackish/salt groundwater is caused by mixing with seawater trapped within clay layers; and 2) brackish/salt surface waters result from seepage of brackish groundwater into rivers and wetlands, followed by evaporation, hence increasing salinity and δ18O values. Mixing with small fractions of trapped seawater as main salinity source, rather than halite dissolution, is further corroborated by Br/Cl ratios of brackish/salt water samples near the ocean ratio. Cation exchange upon salinization is mainly observed in the semi-confined aquifer, while freshening takes place in the phreatic aquifer, particularly in areas presenting high recharge rates.