Studies that focus on the flow dynamics in multi-channel estuaries using detailed field measurements are rarely reported. Hence, this study investigates the effect of changes in topographic features on the upstream fluvial patterns and downstream salinity intrusion at the multi-channel Tanintharyi River estuary (TRE), Myanmar. The outcomes were compared with the multi-channel Chikugo River estuary (CRE) and Arakawa River estuary (ARE) of Japan using the data presented in previous studies. Continuous measurements of velocity and discharge distributions were conducted at 12-h intensive surveys (30-min intervals) at the upstream confluence area of TRE during spring and neap tides. The velocity in the TRE was vertically uniform during spring and neap tides. The maximum horizontal velocity was found at the middle area of the main channel and at the thalweg area of the branch. In TRE, the discharge ratio of the branch to total discharge was temporally changed during a tidal cycle while the area ratio was stable. Conversely, the discharge ratio of the branch to total discharge in the CRE was nearly equal to the area ratio of the branch. This may be due to the influence of channel sinuosity. The mean velocity in the upstream estuarine channel reduced with an increase in sinuosity index (SI) in both TRE and CRE. Hence, the SI has a negative influence on the upstream fluvial flow. Further, the saltwater travel distance in the three multi-channel estuaries (TRE, CRE, and ARE) increased with a decrease in SI. Conversely, the salinity intrusion length in all three estuaries increased with an increase in SI. This shows that the SI has a negative influence on the saltwater travel distance and a positive influence on the salinity intrusion length. In conclusion, the topographic features of estuaries have a strong and different impact on the flow dynamics in their upstream and downstream.