The role of the fine-dune sand dynamics in controlling the natural regeneration of the upper layer of a riverbed used for filtration is studied at the Choreti test reach of Rio Parapeti, in the Southern sub-Andean zone of Bolivia. Local production of drinking water relies on Riverbed Filtration, the delivery of which depends on the river water depth and the riverbed permeability. There is a strong, natural, declamation process of the upper layer maintained by dune bed-forms migrating downstream. It is thus essential to understand and represent local water depth changes as a function of the incoming discharge. We show the vortex-drag model can be used to correctly calculate the stream velocity in natural environment. Then we study the sand dunes characteristic (wavelength and celerity) in the Rio Parapeti. Because of the shallow-flow configuration the dominant dune length can be easily extracted from satellite images taken at various dates. We also show that it is more than likely that dune movement can be followed by the simple deployment of a pressure probe into the water under stable discharge condition, even if further data and investigation are necessary to confirm this