The atmospheric transport and deposition of aerosols has the potential to influence the chemistry and biology of oligotrophic alpine lakes. In recent decades, dust and nitrogen emissions to alpine ecosystems have increased across large areas of the western U.S., including Wyoming. Here, we use sediment geochemistry and 87Sr/86Sr and 143Nd/144Nd isotopes to examine historical dust deposition rates to alpine lakes in the southwestern region of the Wind River Range, Wyoming. We evaluate the biological response using diatom fossil assemblages and sediment pigment concentrations. Sediment core analyses indicated that prior to a recent rise in dust flux, phosphorus concentrations and species composition were similar to those found in other alpine lakes in the region. Concomitant with a ∼50 fold increase in dust flux to the sediments circa 1940, sediment proxies revealed a two- to threefold increase in normalized sediment phosphorus content, an increase in the diatom-inferred total dissolved phosphorus concentration from ∼ 4 to 9-12 μg L−1, a tenfold increase in diatom production, and a relative increase in cyanobacteria abundance. The increase in dust influx during the 20th century appears to be due in part to human factors and demonstrates the potential for dust and other atmospheric pollutants to significantly alter remote aquatic ecosystems.