Driven by interactive multiscale motions, the water exchange between the Pearl River Estuary (PRE) and coastal seas exhibits complex spatial structures and significant temporal variability. In this study, the exposure time (θ‾) was calculated using the adjoint method to examine the spatiotemporal characteristics of water exchange and illustrate the substance movement pathway in the PRE and the adjacent shelf. Seasonal variations in water exchange are generally determined by subtidal motion in the estuary and adjacent shelf. In summer, the θ‾ gradually increases from approximately 5 days near the lower estuary to 15 days in the upper estuary. In winter, associated with the weaker river discharge and prevailing northeasterly winds, the water exchange is suppressed and θ‾ increases to approximately 35 days in the upper estuary. Owing to the surface/bottom subtidal offshore/onshore transport in the water column, the θ‾ of the bottom water increases by 10 days compared to the surface water. Outside the estuary, the seasonally reversing shelf current and onshore transport move the shelf substance back into the PRE. The θ‾ to the southwest and northeast of the PRE is approximately 5 and 10 days in summer and winter, respectively. Temporally, the interplay between the periodic tidal motion and shelf current induces a significant intra-tidal variation of θ‾, predominantly in the middle estuary, where the water exchange is sensitive to the initial release time. The θ‾ with the initial release time of high/low tide generally has shorter/longer values. The intra-tidal variation of θ‾ is approximately three days and two weeks in summer and winter, respectively. The distinct three-dimensional structure and intra-tidal variability of water exchange illustrated in this study help to better utilize fluid motion that refreshes the water inside the estuary.