The deposition of dust has recently increased significantly over some regions of the western US. Here we explore how changes in dust deposition have affected the biogeochemistry of two alpine watersheds in Colorado, US. We first reconstruct recent changes in the mass accumulation rate of sediments and then we use isotopic measurements in conjunction with a Bayesian mixing model to infer that approximately 95% of the inorganic fraction of lake sediments is derived from dust. Elemental analyses of modern dust indicate that dust is enriched in Ca, Cr, Cu, Mg, Ni, and in one watershed, Fe and P relative to bedrock. The increase in dust deposition combined with its enrichment in certain elements has altered the biogeochemisty of these systems. Both lakes showed an increase in primary productivity as evidenced by a decrease in carbon isotopic discrimination; however, the cause of increased primary productivity varies due to differences in watershed characteristic. The lake in the larger watershed experienced greater atmospheric N loading and less P loading from the bedrock leading to a greater N:P flux ratio. In contrast, the lake in the smaller watershed experienced less atmospheric N loading and greater P loading from the bedrock, leading to a reduced N:P flux ratio. As a result, primary productivity was more constrained by N availability in the smaller watershed. N-limited primary productivity in the smaller watershed was partly ameliorated by an increase in nitrogen fixation as indicated by reduced nitrogen isotopic values in more contemporary sediments. This study illustrates that alpine watersheds are excellent integrators of changes in atmospheric deposition, but that the biogeochemical response of these watersheds may be mediated by their physical (i.e. watershed area) and chemical (i.e. underlying geology) properties.