Interannual differences in the water quality of Anvil Lake, WI, were examined to determine how water level and climate affect the hydrodynamics and trophic state of shallow lakes, and their importance compared to anthropogenic changes in the watershed. To determine how changes in water level may affect these processes, the General Lake Model (GLM) was used to simulate how the lake’s thermal structure should change in response to changes in water level using R. This dataset includes the data inputs to the GLM model and the direct outputs from the model. Model Calibration (GLM_CalibrationZ); Simulation of with Deep Lake and Cold Weather (GLM_Deep_Cold_SimulationZ); Simulation of with Deep Lake and Hot Weather (GLM_Deep_Hot_SimulationZ); Simulation of with Shallow and Hot Weather (GLM_Shallow_Hot_SimulationZ); Simulation of with Shallow Lake and Cold Weather (GLM_Shallow_Cold_SimulationZ).