Three eutrophication models (mass balance, BATHUB, and Jensen models) were developed and calibrated for the Winnebago Pools, Wisconsin. These models were used to quantify the input of phosphorus from the sediments of the lakes, and determine how the water quality (total phosphorus concentration, chlorophyll a concentrations, and Secchi depth) should respond to changes in phosphorus loading from the watershed. Each of the models were developed using flow and phosphorus inputs from internal and external sources. This data release is subdivided into 4 parts: 1) Lake Winnebago water-quality data; 2) Mass balance of water and phosphorus for Lake Winnebago, with estimated internal loading of phosphorus estimates; 3) BATHTUB model inputs and outputs ; and 4) Jensen model inputs and outputs.