Little Shingobee Lake and Fen are part of the extensive network of lakes and wetlands in the Shingobee River headwaters of northwestern Minnesota, designed to study the interactions between surface and ground waters. Prior to about 11.2 cal. ka, most of these lakes and wetlands were interconnected to form glacial Lake Willobee, which apparently formed when a debris flow dammed the Shingobee River. Between 11.2 and 8.5 cal. ka, the level of Lake Willobee fell as a result of breaching of the dam, transforming the deep lake into the existing lakes and wetlands. Analyses of a 9-m core from Little Shingobee Lake (LSL-B), and lacustrine sediments under 3.3 m of peat in a 17-m core from Little Shingobee Fen (LSF-10), show that the dominant components are allogenic clastic material, and endogenic CaCO₃ and organic matter. In both cores almost all of the iron (Fe) and manganese (Mn) are incorporated in endogenic minerals, presumed to be X-ray amorphous oxyhydroxide minerals, that occur in significant quantities throughout the cores; almost no Fe and Mn are contributed from detrital aluminosilicate minerals. This suggests that, for most of the Holocene, the allogenic watershed contributions to lake chemistry were minor compared to the dissolved mineral load. In addition, prior to 3.5 cal. ka, pollen zone boundaries coincide with large changes in lake-sediment mineralogy, indicating that both landscape and climate processes were linked to early- and mid-Holocene lake chemistry. The pollen time series, with sequential domination by spruce, pine, sagebrush-oak, birch-oak and, finally, white pine is typical of the region and reflects the changing location of the prairie-forest transition zone over time. These changes in vegetation had some profound effects on the geochemistry of the lake waters.