The Winnebago Pool is a chain of 4 shallow lakes in Wisconsin. Because of high external phosphorus (P) inputs to the lakes, the lakes became highly eutrophic, with much P contained in their sediments. In developing a total maximum daily load (TMDL) for these lakes, it is important to determine how their phosphorus concentrations should respond to changes in external P loading. In many TMDLs, internal P loading is assumed to be negligible or it is estimated based on sediment release rates and dissolved oxygen conditions in the lake, and each lake is considered independently. To evaluate these assumptions, internal P loading and external P loading were quantified by developing detailed P budgets for the Winnebago Pool chain of lakes. This information was then inputted into 2 eutrophication models (BATHTUB and Jensen models), which were used to simulate the steady-state and transient effects of various P reduction strategies. The importance of internal P loading varied among lakes, from being a minor source to representing almost 60% of the summer P input. Model results indicate that each lake responds to external P reductions, but internal loading can delay the lake responses, especially in the most downstream lake, Lake Winnebago, where internal P loading was most important to its summer P budget. Accurately quantifying net internal P loading and using this information in lake models are important in evaluating how large shallow lakes should respond to P reduction strategies, setting realistic expectations from watershed P reductions, and guiding TMDL efforts.