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With the increasing demand for water resources, the utilization of marginal water resources of poor-quality has become a focus of attention. The brackish water developed in the Loess Plateau is not only salty but also famous for its “bitterness”. In the present work, multi-isotope analysis (Sr, B) was combined with geochemical analysis to gain insight into the hydrogeochemical evolution and formation mechanisms of brackish water. These results demonstrate that groundwater in the headwater is influenced by carbonate weathering. After the confluence of several tributaries in the headwater, the total dissolved solids (TDS) of water is significantly increased. The dissolution of evaporates is shown to be the main source of salinity in brackish water, which also greatly affects the Sr isotopic composition of water. This includes the dissolution of Mg-rich minerals, which is the main cause of the bitterness. Furthermore, the release of calcium from the dissolution of gypsum may induce calcite precipitation and incongruent dissolution of dolomite, which also contributes to the enrichment of magnesium. The highly fractionated boron isotopic values observed in the upstream groundwater were explained by boron interacting with clays, illustrating the important role played by the cationic exchange reaction. The inflow of brackish groundwater is the source of the observed quality of the river water. River water with relatively enriched 11B contents reflects the occurrence of evaporation along the flow path of the river. This process further aggravates the salinization of river water, with water quality evolving to saline conditions in the lower reach. When the river reaches the valley plain, the 87Sr/86Sr ratios decreases significantly, which is primarily related to erosion of the riverbanks during runoff. These results indicate that water resource sustainability could be enhanced by directing focus to mitigating salinization in the source area of the catchment.