The dynamics of water levels, transverse channel deformations, and redistribution of water discharges along the branches of the Volga River, both during planned industrial sand mining and during extreme transformation of the bottom topography in the area of the quarry, have been studied. A real quarry of non-metallic building materials was considered, located at the mouth of the Volozhka Partridge of the Volga — Akhtuba floodplain (VAF) in the section 2549–2550 km of the Volga River. Mathematical modeling of the joint dynamics of shallow waters, traction and suspended sediments is carried out, which takes into account the nonlinear dynamics of the liquid and bottom deformations. For the numerical solution of the Saint-Venant and Exner equations, the CSPH-TVD method was used, the parallel CUDA algorithm of which is adapted for highperformance computing on supercomputers with graphics coprocessors (GPUs). It is shown that the conditions of quarry development, both during planned mining and under extreme bottom deformation, do not significantly affect the structure of channel flows along shipping routes.