This dataset contains daily concentration data for total phosphorous and daily production data for milk in a South Florida, USA, watershed. The dataset is being provided to improve understanding of an analysis of the relationships between total phosphorous in Lake Okeechoebee, FL, USA, and the relative amount of agricultural activity in the lake's contributing basin. The dataset also contains the output of an specific form of empirical mode decomposition and resultant intrinsic mode functions that can be used to differentiate behavior on various time scales. As a dataset of over 47 years, the datasets provides insight into how changes in agricultural production may be influencing lake water quality, which is useful for understanding contributions to water quality and anticipated trends in the coming decade. For clarity, the dataset consists of a metadata file explaining acronyms and units, the date file as a time series of daily values, and two additional files containing the daily residuals and values derived from the intrinsic mode functions for each datatype. The specific method of analysis is described in the associated publication.