This chapter examines the uncertainties inherent in the water and chemical budgets of the lake in relation to the differences between chemical mass change in storage and to the balance between solute inputs and solute outputs associated with water fluxes. It begins by discussing uncertainty in the water budgets used to determine chemical budgets. It then examines uncertainties in chemical analyses of precipitation samples, surface water samples, and groundwater samples. It also discusses alternative approaches to determining chemical budgets. It describes the methods used to calculate chemical mass input from the tributaries, chemical mass loss by surface outflow, chemical mass input from groundwater, and chemical mass loss by flow through groundwater.