Williams and Shingobee lakes are at opposite ends of the local ground water flow system in the Shingobee River Headwaters Area (SRHA) in north‐central Minnesota. Williams Lake, situated near the highest point in the flow system, has no surface inlet or outlet, and ground water and precipitation are the only sources of water. Shingobee Lake, situated at the lowest point in the flow system, has the Shingobee River as an inlet and outlet. Ground water directly contributes an estimated one‐fourth of the water input to Shingobee Lake. The Shingobee River also receives large amounts of ground water discharge along its reach to Shingobee Lake providing a large, indirect source of ground water to the lake. Differences in nutrient concentrations reflect the residence times and nutrient supplies of these two lakes. The average phosphorus content of Shingobee Lake is about twice that of Williams Lake. Consequently, phy‐toplankton productivity in Shingobee Lake is much higher than in Williams Lake, leading to an oxygen‐deficient (<1 ppm dissolved oxygen) hypolimnion within a month after overturn in both the spring and fall. Because of the extreme reducing conditions in the hypolimnion of Shingobee Lake, high concentrations of dissolved iron and manganese are present there during summer stratification. In some years, the manganese concentration in the hypolimnion of Shingobee Lake remains high throughout the year. Precipitation of iron and manganese minerals, presumed to be X‐ray amorphous oxyhydroxides, at periods of fall and spring overturn result in concentrations of iron and manganese in surface sediments of Shingobee Lake that are seven times and 27 times higher, respectively, than can be explained by contributions of iron and manganese from detrital aluminosilicates. These findings indicate that the source and amounts of this excess iron and manganese found in the sediments are correlated to the amount of iron‐ and manganese‐rich ground water discharging to Shingobee Lake. Because iron and manganese oxyhydroxides are efficient adsorbers of phosphorus, concentrations of phosphorus are also high in the sediments of Shingobee Lake. Without this sequestration of phosphorus, the productivity of Shingobee Lake would probably be much higher.