Circulation of saline water is important for maintaining water quality in the Ganges-Brahmaputra-Meghna (GBM) delta because of its vulnerability to the threat of climate change. We applied a numerical model to examine the volume and salt transports within the GBM delta, Bangladesh. To understand the components of salt water intrusion driven by tidal and subtidal (residual) transports, we selected 19 cross-sections to represent the complex delta circulation in a simplified network model. Our results show that over 82.51% of GBM river water drains through the eastern estuarine system (EES) in the wet season, increasing to 98.37% in the dry season. Residual transport can be comparable in size with the tidal transport in the wet season, and one order of magnitude smaller in the dry season. The western estuarine system (WES) experiences serious salinity intrusion in the dry season, and strong seasonal variability in both tidal and subtidal transport, with suppression of tide-driven transport observed during the wet season. Our results show the sub-channels area of the Lower Meghna River also faces the risk from salinity intrusion issues, as stronger tidal salt flux is estimated in the dry season. Tidal volume transport varies seasonally, corresponding to the variability of river discharge. A simplified solution by means of polynomial expansion was applied to describe the tidal propagation within river channels. Inland penetration of tidal energy is reduced with large river discharge, and additionally the propagation speed of the tidal wave increases in the wet season. Our analysis helps understand the response of the three estuarine systems to seasonal and tidal controls, and can be used to inform river management about the upstream-downstream linkages.