Concentrations and loads of total phosphorus, dissolved phosphorus, and suspended solids were estimated for three sites on the Lower Fox River for October 1988 through September 2021. The sites are the Fox River at Neenah-Menasha (040844105), Fox River at DePere (04085059), and Fox River at the Mouth (040851385). Data analysis was conducted with the Weighted Regressions on Time, Discharge, and Season (WRTDS) method. Daily loads were estimated using the WRTDS method with Kalman filtering. To determine changes in loads over this period, the annual load results were flow-normalized to standardize for the varying flow dynamics that occurred among years. The model archive contains the R code for running the WRTDS model, functions used by the R code, and the input data files. The output folder contains WRTDS model output summarized by 1) water year, 2) water year and season, and 3) water year, season, and three specified values of discharge. The models folder contains the WRTDS model objects. This dataset includes a separate file with all phosphorus, nitrogen, and suspended solids sample data for the three study sites from 1973 to 2022. This file includes a column indicating who collected the samples.