Lowlands are vulnerable to flooding due to their mild topography in often densely populated areas with high social and economic value. Moreover, multiple physical processes coincide in lowland areas, such as those involved in river-sea interactions and in merging rivers at confluences. Simultaneous occurrence of such processes can result in amplifying or attenuating effects on water levels. Our aim is to understand the mechanisms behind simultaneous occurrence of discharge waves in a river and its lowland tributaries. Here, we introduce a new way of analyzing lowland discharge and water level dynamics, by tracing individual flood waves based on dynamic time warping. We take the confluence of the Meuse River (∼ 33000km2) with the joining tributaries of the Dommel and Aa rivers as an example, especially because the January 1995 flood at this confluence was the result of the simultaneous occurrence of discharge peaks in the main stream and the tributaries and because independent observations of water levels and discharge are available for a longer period. The analysis shows that the exact timing of the arrival of discharge peaks is of little relevance because of the long duration of the average discharge wave compared to typical time lags between peaks. The discharge waves last on average 9 days, whereas the lag time between discharge peaks in the main river and the tributaries is typically 3 days. This results in backwaters that can rise up to 1.5 m over a distance of 4 km from the confluence. Thus, local measures to reduce the impact of flooding around the confluence should account for the long duration of flood peaks in the main system.