Saline groundwaters are common to inland Australia, but their hydrochemical evolution and origin remain largely unknown. The saline groundwaters in the alluvial aquifers of the Darling River have previously been found to exhibit broad similarity in traditional hydrochemical and isotopic tracers. By contrast, in this study the trace element isotopes (delta Li-7, delta B-11 and Sr-87/Sr-86) have illuminated more complex hydrogeochemical processes in the same aquifer system. This paper reports the first ever set of delta Li-7 values in any groundwater system in Australia. They varied from +5.8 to +16.2 with an average value of +9.7 parts per thousand (n = 19) in the alluvial aquifers of the Darling River catchment. The delta B-11 values were all higher than seawater and close to some of the highest delta B-11 values ever reported in the literature for a groundwater system (+44.4 to +53.9; average: +48.8, n = 17). The Sr-87/Sr-86 ratios ranged from 0.708 to 0.713, with an average value of 0.709 (n = 19). The differing signatures in these trace element isotope values, highlighted by discovery of the deeper older groundwater system with heavier Li isotope values and higher Sr-87/Sr-86, is an important finding of this research. Simple mixing models between river water and saline groundwater cannot explain the observed variation in trace element isotopes. Hydrochemical evolution was found to be dependent on proximity to the Darling River and depth. Varying degrees of Li and B isotopic fractionation during water-sediment interaction were interpreted to account for the evolution of the saline groundwaters. The measurement of these trace element isotopes has permitted delineation of groundwater end-members that would have otherwise not been identified; in their absence an inaccurate interpretation of the hydrochemical evolution of these saline groundwaters would have been made. This study highlights the importance of a multi-tracer approach, which includes trace element isotopes, in resolving complex geochemical processes in groundwater in semi-arid to arid zone environments. © 2013, Elsevier Ltd.