River flow can be continuously monitored through velocity measurements with an acoustic Doppler current profiler, deployed horizontally at a river bank (H-ADCP). This approach was adopted to obtain continuous discharge estimates at two cross-sections in the River Mahakam, i.e. at an upstream station located about 300 km from the river mouth and at a downstream station located about 15 km from the river mouth in the Mahakam delta. We applied both the standard index velocity method and a recently developed methodology to obtain a continuous time-series of discharge from the H-ADCP data. Measurements with a boat-mounted ADCP were used for calibration and validation of the model to translate H-ADCP velocity to discharge. The new method accounts for the dip in velocity near the water surface, which is caused by sidewall effects that decrease with the width to depth ratio of a channel. A boundary layer model is introduced to convert single depth velocity data from the H-ADCP to specific discharge. A regression model is employed to translate specific discharge to total discharge. The upstream discharge station represents an area influenced by variable backwater effects from lakes, tributaries and floodplain ponds, and by tides. Discharge rates at this station exceeded 3250 m3 s ˆ’1. Backwater effects from lakes were shown to be significant, whereas interaction of the river flow with tides systematically impact discharge variation. Despite the complexity of feedbacks between the river flow and the tidal motion, tides are shown to have a predictable modulating effect on discharge, which is most apparent in the fortnightly frequency band. At the downstream station, discharge rates exceeded 8000 m3 s ˆ’1. Intratidal variations were most obvious during bidirectional flow conditions, which occurred only during conditions of low river discharge. The new method was shown to outperform the widely used index velocity method in these poorly gauged sites.