The impact of topography and tidal forcing on counter-current flow formation in monsoon-affected multi-channel macrotidal river estuaries is seldom studied. This research investigates the occurrence of counter-current flow during the monsoon season, characterized by strong semi-diurnal tidal currents, at the confluence area of the complex multi-channel macrotidal Tanintharyi River estuary (TRE) in Myanmar. Continuous measurements of velocity and discharge, along with surveys of topography and water quality (salinity, turbidity), were conducted during a 12-hour intensive survey (30-minute intervals) at the upstream junction area of the main channel and the branch during the spring tide. The main channel's width, approximately four to five times larger than the branch's width, experiences counter-current flow during ebb tide when water levels between the two channels are similar. Despite the freshwater environment and stable turbidity indicated by vertical profiles, tidal effects still influence counter-current flow formation. The imbalance in area and discharge ratios between the main channel and branch can be attributed to another important factor: downstream topography. The main channel with wide (1.3 km), straight (SI: 1.1), and short (28 km) topography, is highly sensitive to tides compared to branch with the narrow (180 m), meandering (SI: 2.1), and long (40 km) topography. The difference in downstream topography between the main channel and branch, combined with tidal forcing, plays a crucial role in counter-current flow formation in the upstream junction area of the TRE.