The potential of environmental tracers (δ18O, δ2H, δ13C, 14C, 4He, 20Ne, 40Ar, N2) to assist our understanding of recharge processes, groundwater flow velocities and residence times in semi-confined, multilayered and faulted aquifer systems was tested in a coastal system with Quaternary sediments overlying Tertiary aquifers and fractured bedrock. Carbon-14 groundwater ages were found to increase with depth and distance (<1000 y near the recharge area to >30,000 y near the coast), confirming that the system is semi-confined and the palaeometeoric origin of groundwater as suggested by water stable isotopes. The presence of old groundwater near the top of deep semi-confined aquifers suggests that recharge mainly occurs in the ranges east of the basin. This is also supported by Cl concentrations, which are higher in the overlying Quaternary aquifers. Groundwater flow velocities between 0.3 and 1.8 m y−1 were estimated using 14C ages, resulting in basin recharge estimates between 0.3 × 107 and 2 × 107 m3 y−1. Radiocarbon and 4He-estimated flow velocities were generally in good agreement, although 4He accumulation rates ranging between 8 × 10−12 and 1 × 10−10 cm3 STP g−1 y−1 and 1.7–7.1 × 10−7 cm3 STP g−1 km−1 confirmed slower flow velocities in some areas. These areas could not be captured using 14C. Faults were found to play a paramount role on mixing old fluids rich in salts and 4He, although it was not possible to demonstrate the role of faults in changing flow velocities, this requiring a higher density of sampling points. Our study shows that environmental tracers have potential to study flow processes in semi-confined, faulted, multilayered aquifer systems, provided a high density of sampling points is available.