This study experimentally and numerically investigated the mixing processes at a notched weir to examine the relationship between the mass exchange coefficient and geo-hydraulic factors of notched weirs. Laboratory experiments on idealized notched weirs with variable notch spaces, notch heights, and hydraulic factors were performed to measure the flow field dynamics and depth-averaged concentration fields of the solute tracer. The experiment results demonstrated that flow separations occurred upstream of the notched weir. These flow structures controlled the horizontal storage zone and tracer mixing between the main flow and storage zone. The tracer cloud exhibited a longer retention time as the storage zone area increased. The normalized value of measured mass exchange coefficients by mean flow velocity, ke /Umean ranged from of 0.11 to 0.25, approximately one order larger than the values obtained in previous studies on lateral transient storage zones, such as lateral groin fields, and cavities, which implied that the notched weir in this study generated a storage zone with a fast exchange process and relatively weak storage effect. Numerical simulations with expanded geometric and hydraulic conditions revealed that the mass exchange coefficient was strongly correlated with the geometric factors, such as the notch space and height, and hydraulic factors, such as the Froude and Reynolds numbers. An empirical relationship applicable to rivers with notched weir structures under low-flow conditions (Fr < 0.1) was proposed based on the experiment and numerical results. The performance of the proposed empirical relationship showed a satisfactory level of R2 of 0.87. This relationship can be applied as a tool for estimating the mass exchange coefficient of notched weirs using easily measurable field data in rivers.