The dataset contains measurements of total phosphorus (P) flux rates between bottom sediments and the overlying water column for Green Valley Lake, a hypereutrophic reservoir in southwest Iowa, USA. Flux measurements were made using ex situ sediment core incubations. Intact sediment cores and the overlying water were collected at three sites along the longitudinal gradient of the reservoir in July of 2019 and February, April, June, August, and October of 2020 in order to assess spatiotemporal variation in sediment P flux rates. Cores were incubated under ambient temperature and dissolved oxygen conditions for 4-5 days. Daily measurements of total P in the overlying water were used to calculate areal P flux rates on a daily timestep. The dataset includes a table of raw total P concentrations, temperature, dissolved oxygen, and pH of the overlying water throughout the incubations, an r script detailing necessary calculations and cleaning procedures, and a final data table with calculated P flux rates. The dataset will be used to identify hot spots and hot moments of sediment P release in Green Valley Lake, which will contribute to our understanding of how areas of lakebed and times of the year can disproportionately influence whole-lake water chemistry. Additionally, the data tables and script provide an example of how to calculate P flux rates from sediment core incubations while accounting for artificial changes in water column total P concentrations due to daily sampling.