Hypolimnetic hypoxia, or low oxygen in bottom waters, impairs ecosystem services of freshwater lakes and estuaries globally. Both hypoxia incidence and intensity are increasing around the world due to eutrophication and climate change. As the hypolimnion becomes hypoxic and ultimately anoxic, sediment-bound legacy phosphorus is released. Water column mixing due to large storm events or fall turnover entrains these nutrients to the surface, causing harmful algal blooms. To assess the dynamics of hypoxia throughout the growing season, we evaluated Muskegon Lake, where hypoxia recurs annually, utilizing high-frequency time-series data from the Muskegon Lake Observatory (MLO) buoy (https://www.gvsu.edu/wri/buoy/), biweekly nutrient sampling, and seasonal respiration experiments during 2021. While water-column stratification set the stage for hypolimnetic hypoxia, frequent wind-mixing events, and episodic intrusions of cold, oxygenated, upwelled Lake Michigan waters intermittently reduced the thickness or intensity of the hypoxic zone. Respiration experiments revealed that riverine and surface organic matter inputs contributed most to hypolimnetic hypoxia in the spring, whereas surface inputs did so during summer, and riverine inputs during fall, indicating seasonally variable sources drive hypoxia. Biweekly measurements indicated increased soluble reactive phosphorus in the hypolimnion during anoxia via internal phosphorus loading from the sediment with the potential for fueling surface blooms with net export of soluble reactive phosphorus and total phosphorus to nearshore Lake Michigan. Our findings on the role of seasonally changing temperature, loading, phytoplankton production, hypolimnetic respiration, and internal phosphorus loading in shaping hypoxia dynamics have relevance to similarly afflicted ecosystems in the Great Lakes Basin.