Subtidal water level dynamics in the Berau river, East Kalimantan, Indonesia, feature a pronounced fortnightly variation. The daily mean water levels at a station about 60 km from the sea are 0.2–0.6 m higher during spring tide than during neap tide. To explain the underlying mechanisms, a local subtidal momentum balance is set up from field data, using continuous discharge estimates inferred from measurements taken with a horizontal acoustic Doppler current profiler. It is demonstrated that terms accounting for friction and variation in the water surface gradient are dominant in the subtidal momentum balance. To further investigate the sources of subtidal water level variation, a generic method of analysis is proposed to decompose the subtidal friction term into contributions caused by river flow, by interaction between tidal motions and river flow, and by the tidal motions alone. At the station under study, mainly the river-tide interaction term is responsible for generating fortnightly variation of the subtidal water level. The contribution from interaction between diurnal, semidiurnal, and quarterdiurnal tides to subtidal friction is significantly smaller. Provided that the reduction of tidal velocity amplitudes with increasing discharges can be predicted from a regression model, the results presented herein can be used to predict changes in subtidal water levels as a result of increased river discharges.