The Ljubljana Marshes (Ljubljana Moor) is a large wetland in the southern part of the Ljubljana basin in the central part of Slovenia, with well-preserved archaeological evidence of settlements. The data have traditionally been interpreted as the remnants of the prehistoric pile dwelling settlements located in a shallow lake. In this paper, we present new data that challenge these interpretations. An aerial LiDAR survey of the Ižica floodplain on the Ljubljana Marshes has revealed a complex topography of stratified palaeochannels. The 14C dates of the channel infills suggest that the first phase of the palaeochannels can be dated to before 3770 cal. BC, which is contemporary with Eneolithic settlements located on its banks. We suggest that settlements were located in the floodplain, next to active rivers, and not in the lake as was traditionally hypothesised.