Abstract Accurate estimation of hydrogeological parameters is essential for groundwater modeling but largely depends on the quality of tracer data. Traditional tracers, including dyes and ions, are constrained by signal interference, a narrow selection of options, and poor detection sensitivity. This study investigated synthetic DNA fragments as high‐resolution tracers in replicated two‐dimensional sandbox experiments. Eight uniquely sequenced DNA tracers were co‐injected with dye tracers and assessed using two frameworks: tracer travel‐time inversion (TTTI) and a two‐step approach combining TTTI with hydraulic tomography. DNA tracers produced clearer breakthrough signals and achieved consistently higher accuracy (R2 values of 0.75 and 0.75 for twice TTTI; 0.79 and 0.76 for twice two‐step approach), whereas dye tracers yielded lower and more variable R2 values (0.64 and 0.59; 0.75 and 0.56). These findings demonstrate that DNA tracers, with high specificity and sensitive detection, enable a robust pathway for improving hydrological parameter inversion.

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