Diatom assemblages in sediments from two subalpine lakes in the Uinta Mountains, Utah, show asynchronous changes that are related to both anthropogenic and natural inputs of dust. These lakes are downwind of sources of atmospheric inputs originating from mining, industrial, urban, agricultural and natural sources that are distributed within tens to hundreds of kilometers west and south of the Uinta Mountains. Sediment cores were retrieved from Marshall and Hidden lakes to determine the impacts of atmospheric pollution, especially metals. Paleolimnological techniques, including elemental analyses and ²¹⁰Pb and ^239+240Pu dating, indicate that both lakes began receiving eolian inputs from anthropogenic sources in the late 1800s with the greatest increases occurring after the early 1900s. Over the last century, sediments in Marshall Lake, which is closer to the Wasatch Front and receives more precipitation than Hidden Lake, received twice the concentrations of metals and phosphorus as Hidden Lake. Comparison of diatom and elemental data reveals coeval changes in geochemistry and diatom assemblages at Marshall Lake, but not at Hidden Lake; however, a major shift in diatom assemblages occurs at Hidden Lake in the seventeenth century. The change in diatoms at Marshall Lake is marked by the near disappearance of Cyclotella stelligera and C. pseudostelligera and an increase in benthic, metal-tolerant diatoms. This change is similar to changes in other lakes that have been attributed to metal pollution. The marked change in diatom assemblages at Hidden Lake indicates a shift in lake-water pH from somewhat acidic to circumneutral. We hypothesize that this change in pH is related to drought-induced changes in input of carbonate-rich desert dust.