Interannual differences in the water quality of Anvil Lake, Wisconsin, 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. Anvil Lake is a relatively pristine seepage lake with hydrology dominated by precipitation, evaporation, and groundwater exchange enabling the typically subtle effects of water level and climate to be evaluated. Groundwater and hydrodynamic models were used to describe lake water and phosphorus budgets and how its hydrodynamics are affected by water level and air temperature. Decreases in water level are expected to cause Anvil Lake and other shallow lakes to stratify fewer days, and have warmer bottom temperatures and more deep-mixing events. Increasing air temperatures should cause these lakes to have shorter ice cover, longer summer stratification periods, and warmer bottom temperatures. How water level affects water quality depends on how nutrient loading and lake volume vary: during drier, low-water years, lakes with large interannual changes in loading should have better water quality, whereas lakes with small changes in loading should degrade slightly. Anthropogenic changes in Anvil Lake's watershed over the past ∼100 yr were about 1.5 times the effects of changes in water level when levels were low, but the effects were similar when levels were high. Climate warming is expected to increase productivity in shallow lakes because warmer air temperatures will likely increase bottom temperatures increasing sediment phosphorus release and deep-mixing events enabling this phosphorus to reach the epilimnion.