Net water transport (NWT) in estuaries is important for, for example, salt intrusion and sediment dynamics. While NWT is only determined by river runoff in single channels, in estuarine networks, it results from a complex interplay between tides and residual flows. This study aims to disentangle the various contributions of these physical drivers to NWT in estuarine networks and investigate the sensitivities of NWT to variable forcing conditions, interventions, and sea level rise (SLR). To this end, a processes-based perturbative network model is developed, which accounts for the vertical flow structure to resolve density-driven flow driven by a vertically uniform along-channel salinity gradient. Other identified drivers are river discharge and three tidal rectification processes: Stokes transport and its return flow, momentum advection, and velocity-depth asymmetry. The model is applied to the Yangtze Estuary. NWT due to tidal rectifications and density-driven flow can be comparable to river discharge. Specifically in the North Branch, the direction of NWT may differ from the direction of river discharge. Varying river discharge mainly affects NWT as tide-river interaction is weak and density-driven flow is shown to be insensitive to salt intrusion. Conversely, variations in tidal amplitude strongly affect NWT related to tidal rectification and density-driven flow. The deepening (narrowing) of one channel (Deep Waterway Project), affected the NWT mostly through the density-driven flow (advection). Furthermore, NWT distribution in the Yangtze is insensitive to SLR up to 2 m because the effects of SLR on transport due to different drivers compensate each other
