Water quality and hypoxia in lakes and reservoirs are strongly associated with water renewal. Yet vertical water exchange is still not fully understood and challenging to evaluate in highly dynamic systems. Here, we applied a scaling approach using the vertical timescale, vertical water age (VWA), defined as time since a water parcel last touched the water surface. We established a 3D hydrodynamic-based age model to quantify the vertical water renewal in Xiangxi Bay, a tributary bay of the Three Gorges Dam. The integrated effects of hydrodynamic processes like stratification, intruding density currents from the mainstream, and upstream inflow on the vertical renewal were accounted for. Results indicated that the spatial–temporal distribution of VWA in Xiangxi Bay depended on stratification and forms of intruding density currents. Age was large in spring and summer, and small in autumn and winter, reaching a maximum of 25 days in April. The vertical water renewal was faster during bottom intrusions from the mainstream than during middle and surface intrusions. At times, the epilimnion contained old water due to circulations, and the hypolimnion contained young water due to upstream flushing. In contrast to natural lakes, the bottom water was often younger than overlying intermediate waters. This demonstrated that mixed layer depth was insufficient to fully capture the vertical exchange in riverine systems with significant surface/bottom intrusion. The findings suggested VWA as a quantitative measure of vertical water transport in highly dynamic systems and its usability for environmental water management.