Williams Lake, Minnesota is a closed‐basin lake that is a flow‐through system with respect to ground water. Ground‐water input represents half of the annual water input and most of the chemical input to the lake. Chemical budgets indicate that the lake is a sink for calcium, yet surficial sediments contain little calcium carbonate. Sediment pore‐water samplers (peepers) were used to characterize solute fluxes at the lake‐water–ground‐water interface in the littoral zone and resolve the apparent disparity between the chemical budget and sediment data. Pore‐water depth profiles of the stable isotopes δ¹⁸O and δ²H were non‐linear where ground water seeped into the lake, with a sharp transition from lake‐water values to ground‐water values in the top 10 cm of sediment. These data indicate that advective inflow to the lake is the primary mechanism for solute flux from ground water. Linear interstitial velocities determined from δ²H profiles (316 to 528 cm/yr) were consistent with velocities determined independently from water budget data and sediment porosity (366 cm/yr). Stable isotope profiles were generally linear where water flowed out of the lake into ground water. However, calcium profiles were not linear in the same area and varied in response to input of calcium carbonate from the littoral zone and subsequent dissolution. The comparison of pore‐water calcium profiles to pore‐water stable isotope profiles indicate calcium is not conservative. Based on the previous understanding that 40–50 % of the calcium in Williams Lake is retained, the pore‐water profiles indicate aquatic plants in the littoral zone are recycling the retained portion of calcium. The difference between the pore‐water depth profiles of calcium and δ¹⁸O and δ²H demonstrate the importance of using stable isotopes to evaluate flow direction and source through the lake‐water–ground‐water interface and evaluate mechanisms controlling the chemical balance of lakes.