Mathematical models of hydrodynamics and water quality are often used to determine the assimilative capacity of a waterbody when waterbodies violate state water quality standards. A model of the Spokane River and Lake Spokane in eastern Washington was developed to evaluate the assimilative capacity of the waterbody by setting a total maximum daily load (TMDL). A CE-QUAL-W2 model of this system was developed to establish the TMDL limits for the critical low-flow year of 2001. A recent paper evaluated this model and raised several issues about the validity of this model application as a regulatory tool related to its ability to predict total phosphorus, dissolved oxygen, and chlorophyll a relationships. This paper analyzes the validity of their critiques. For example, the critique used an incorrect formula to calculate total phosphorus inflows into Lake Spokane and used a volume-weighted minimum hypolimnetic dissolved oxygen (DOmin) that was not representative of hypolimnetic conditions. They also assumed incorrectly that the hydrologic, meteorological, operational, and sediment conditions of the 2001 TMDL model would be representative of conditions in other years. Although the water quality model of Lake Spokane can be improved, the critique does not invalidate the model as a tool to evaluate how the lake responds to nutrient environmental controls.