Riparian forests belong to the most vulnerable ecosystems worldwide and have been severely affected by logging, livestock grazing and altered flooding over the last decades. Several riparian tree species including Populus spp. face a risk of loss in genetic diversity and associated adaptive potential. A model species for such systems in Central Asia is Populus laurifolia, which in Western Mongolia is commonly confined to river floodplains of the Altai Mountains. Populations appear heavily fragmented and show evidence for lack of regeneration. In order to better understand the ecology of these systems and to provide conservation in the study region and beyond, a total of 615 individuals from first and second order water courses of the Bulgan River in Hovd Aimag were mapped, followed by measurements of diameter at breast height, tree height and sampling of leaf material. Five nuclear microsatellites were employed to estimate standard genetic diversity measures and genetic structure within and among populations. Size class distribution showed a clear sign of over-aging, suggesting that establishment of young individuals is hampered by intense grazing/browsing. Genetic diversity tended to increase downstream, though evidence for genetic differentiation and genetic structuring was ambiguous. This pointed to a time lag between demographic and genetic responses to land use, explained by longevity of trees coupled with clonal growth. As hampered regeneration of plant stands may affect future ecosystem stability, controlled grazing strategies should be considered to secure long-term persistence of stands.