The Rhône delta, South of France (Camargue, 750 km2) is a coastal saline wetland located along the Mediterranean Sea. The confined aquifer of this delta shows high values of electrical conductivity rising from the north (4 mS/cm) to the shoreline (58 mS/cm). This work aims to identify the origin of groundwater salinity and the geochemical processes occurring in this coastal confined aquifer according to the degree of salinity. A natural tracing approach is considered using monthly sampling in 8 piezometers for chemical and isotopic analyses (18O, 2H, 13CTDIC). Ionic and isotopic ratios demonstrate that strong salinities are due to a simple mixing between Mediterranean seawater and freshwater; seawater contribution reaches up to 98% at 8 km from the shoreline. Seawater intrusion induces a particular groundwater chemistry which varies with the degree of seawater contribution: (1) In the less saline part of the aquifer (seawater contribution <20%), the intrusion induces an increase of Na+ in groundwater leading to Ca2+/Na+ exchange processes. The δ13CTDIC analyses show that matrix exchange processes most likely occur for the less saline samples. (2) In the saline part of the aquifer (seawater contribution >20%), the intrusion induces SO4 reduction which is confirmed by highly depleted δ13CTDIC values (up to −19‰). The δ13CTDIC also reveals that methanogenesis processes may occur in the most reductive part of the aquifer. Due to SO4 reduction, the intrusion induces a shift in carbonate equilibrium leading to supersaturation with respect to dolomite and/or magnesian calcite. Thus carbonate precipitation may occur in the area strongly influenced by seawater.