Sediments from Lake Pepin, Minnesota, USA, have been used as provenance tracers to assess hydrology and sediment-transport variations during the Holocene. Lake Pepin is a natural impoundment of the upper Mississippi River, downstream of the confluences with the Minnesota and St. Croix Rivers. Each of the three rivers drains watersheds with distinctly different surficial sediments derived from glacial lobes, which were in turn derived from different bedrock provinces. Geochemical fingerprints for each watershed were determined via ICP-MS analysis of the heavy silt fraction of modern sediment samples. Down-core elemental abundances were compared with these fingerprints using a chemical-mass-balance model that apportions sediment to the source areas. We observed a decrease in the contribution from the Minnesota River watershed during the interval ~6,700 to 5,500 14C yrs B.P.. We interpret the decreased sediment contribution as resulting from decreased discharge of the Minnesota River, which was likely controlled by a combination of precipitation, snow melt, and groundwater input to the river. This hydrologic event coincides with the middle Holocene prairie period observed in fossil pollen data. The presence of this event in a proxy record for hydrologic variations supports the hypothesis that the middle-Holocene prairie period reflects drier conditions than before or after.