The MyLake-Sediment model, available freely on GitHub (https://github.com/biogeochemistry/MyLake_v2_Vansjo), was used to reproduce daily water quality variables and predict sediment-water column exchange fluxes over the boreal Lake Vansjø, Norway. MyLake-Sediment was first used to simulate the impacts of increasing air temperature on algal growth. In another scenario, phosphorus loading from the watershed to the lake was halted in order to quantify the response to internal phosphorus loading. Finally, we simulated the decreasing dissolved phosphate efflux from the sediment when reactive iron was added to the water column. The data contains the input variables used in the modelling study as well as the model output variables.