This article concerns a dynamic model that simulates the main biochemical processes in a milkfish pond that is subject to floating photovoltaic (FPV) cover. The paper includes a model design description that includes details of variable components of the design, including: water temperature, phytoplankton, dissolved oxygen, fish and other variables. Results of the experiment are included, and include: calibration results, ecological effects, and trade-offs between fish and energy production.