The origin of the giant ripple in the Kuray Basin (Altai Republic) is still debatable, and understanding of the process that formed it has not yet been achieved. According to one of the assumptions, it was formed due to the descent of an ice-dammed lake, filled the basin in the Late Pleistocene. It can be clarified by analysing the morphology of the dune field and the internal structure of the individual dunes. We examined the characteristics of all dunes’ morphology from digital elevation models and high-resolution imagery. For the internal stratigraphy of a large number of dunes, we used GPR. We crossed 50 dunes in different parts of the basin with GPR profiles and evaluated several internal structure parameters. A set of parameters, both external and internal, was used for dune classification. By examining the characteristics of the dunes’ morphology and the internal sedimentary structure, we found that giant ripples in the Kuray basin more correspond to the water mechanism of formation rather than aeolian and glacial; the flow velocity varied in different parts of the Kuray Basin, increasing to the north; there is a high probability that the flow has changed direction.