AbstractRiver deltas typically have high population density and support a wide range of intensive and prosperous socioeconomic activities. The hydrological processes in these regions are complex, primarily due to the interactions among the river, aquifer, and sea. However, a systematic and quantitative elaboration of the river‐aquifer‐sea interactions is still lacking. Here, we developed an integrated hydrological flow model for the Pearl River Delta (PRD), which contains the world's largest urban area in both size and population, to gain a deeper understanding of the complexities in the river‐aquifer‐sea interactions. The model performance was validated and cross‐checked via observations at gauging stations and independent remote‐sensing products (e.g., soil moisture, evapotranspiration, and total water storage anomalies). Based on the 10‐year simulation results (2004–2013), the major findings of this study are as follows: (a) accurate representation of the tidal effect is important not only for simulating short‐term flow dynamics but also for capturing the characteristics of long‐term hydrological fluxes and states; (b) the flow‐model‐computed average groundwater discharge rate per unit length of the coastline for the PRD is 3.01 m3/d/m, which is comparable with those derived from water budget approaches but 1–2 orders of magnitude lower than the total submarine groundwater discharge (SGD) estimated by using isotope tracer‐based methods; (c) the temporal variation of SGD is controlled by tidal forcing on an hourly time scale, but by terrestrial hydrological processes on monthly and annual time scales; and (d) an integrated hydrological flow model can be used to identify distinct and large subsurface zones sensitive to tidal fluctuations, quantifying the pivotal role of ocean tides in shaping the coastal groundwater system. This study represents a first step in using an integrated hydrological model to explore river‐aquifer‐sea interactions and their effects on the regional groundwater system simultaneously driven by meteorological and tidal forcings.