Reconstructing water levels reached during past floods contributes to fluvial system understanding and flood risk assessments. For methodological restrictions, this type of research is usually conducted in confined valley settings. In this study, we expand upon that geomorphological context by reconstructing extreme flood levels in a lowland delta setting. We used the archaeological stratigraphy of medieval river cities in the Rhine delta to determine water levels for the largest historic flood in the year 1374. We obtained minimum estimates by identifying thin fluvial deposits interbedded with anthropogenic layers, and further constrained peak flood levels using fourteenth-century raised ground layers directly overlying these deposits. First, we tested the proposed method for extracting flood levels from urban archaeological stratigraphy in the city of Arnhem. Then, we complemented those results with archaeological and historical data in other cities to arrive at a complete overview for the Rhine delta. This overview shows that the 1374 flood levels exceed the highest levels in the instrumental record along the northern distributary (IJssel river), but not along the western distributaries in the central delta (Nederrijn and Waal rivers). This pattern is explained by changes in the discharge division over the different river branches and by the rise of embankments since late medieval times, which considerably decreased the flooded area. Thus, this study demonstrates not only the potential of palaeoflood reconstructions in lowland floodplain settings, but also the pitfalls, resulting from spatially complex flooding patterns and anthropogenic terrain modifications.