The role of large rivers sustaining the civilizations across the world has long been debated. Mapping of palaeochannels using satellite images and the superimposition of known archaeological sites along them are often used as a strong evidence to promote the so called ‘river-culture’ hypothesis. The northwest India has been a hotbed of such studies where a large and wide trace of a palaeochannel (Ghaggar-Hakra channel) mapped from satellite images was linked to the Harappan Civilization, the demise of which was attributed to the decay of a large river (Sarasvati) that once flowed through the region. Recent research involving geophysical surveys and drilling and followed by strong geochronological framework established the subsurface existence of these palaeochannels and their chrono-stratigraphic evolution. However, it was clearly demonstrated that this large palaeochannel was abandoned shortly after ~8 ka and much before the Mature Harappan Civilization developed in this region (~4.6–3.9 ka). These findings strongly contested the contemporaneity of the large river with the Harappan Civilization and instead suggested river avulsion as a major factor for the onset and stabilization of the Harappan culture. Here, we extend this study to further east and examine the palaeochannels related to the Yamuna River that have also been considered to be important tributaries of the large Sarasvati River represented by the Ghaggar-Hakra palaeochannel. At least two of the palaeochannels of the Yamuna have been suggested to be connected to the Ghaggar-Hakra palaeochannel but very limited subsurface evidence exists till date to establish this. Here, we present new, high resolution stratigraphic data based on vertical electrical resistivity soundings (1D–VES), multi-electrode electrical resistivity tomography (2D–ERT), and multi-probe well log surveys in one of the palaeochannels of the Yamuna to map the large-scale geometry and architecture of the valley fills of the palaeochannel system in the subsurface. The geophysical signatures recorded as VES on two transects trending NW–SE in Karnal and Kaithal districts of Haryana at 9 and 13 locations respectively, along with continuous ERT in selected transects reveal the presence of subsurface sand bodies (~10 to >30 m thick) interbedded with silty clay layers that are laterally stacked. The occurrence of thick and wide sand bodies having channel form geometry in the subsurface implies that these are the deposits of a large river system and suggests that the Yamuna was once connected to the palaeo-Ghaggar River as hypothesized by earlier workers based on remote sensing interpretations.