As a critical safeguard for food security in arid regions, water diversion irrigation inevitably triggers dynamic fluctuations in groundwater table. It is therefore essential to clarify the mechanisms of solute transport and accumulation under groundwater table fluctuations (GWTF) to support sustainable development in irrigated areas. This study elucidates the mechanisms from GWTF generation to salt transport and accumulation, and further proposes a dynamic safety threshold for groundwater total dissolved solids (TDS). The findings reveal that pumping, water diversion, and irrigation contribute 25.61%, 26.33%, and 21.37% to changes in the groundwater table, respectively. In terms of fluctuation amplitude, the order is: natural fluctuation group < irrigation fluctuation group < diversion fluctuation group < pumping fluctuation group. Spatial analysis of the hydrodynamic field and salinity distribution indicates a negative correlation between GWTF and groundwater TDS, while a positive correlation exists between groundwater TDS and soil salinity. Quantitative analyses reveal that in high-evaporation environments, groundwater salinization is primarily driven not by direct evaporation, but by external salts from anthropogenic inputs (e.g., fertilizers) and evaporite. Furthermore, GWTF governs the cyclic processes of salt accumulation and re-dissolution. Finally, the Greenberg logarithmic model was applied to quantify TDS safety thresholds under varying GWTF conditions. A key conclusion of this study is that environmentally groundwater TDS thresholds are not static or universal, they vary significantly in response to changing hydrodynamic conditions. This highlights the dynamic nature and environmental dependence of groundwater quality safety standards.