Clear Lake, a hypereutrophic lake, has been beset by recurrent harmful algal blooms for over a century despite reductions in external phosphorus (P) loadings. Internal P loading from sediments may be an additional nutrient source supporting cyanoHABs but is rarely quantified or compared with external loads. During a three year-study from 2019-2021 we calculated both external and internal P loads and determined that internal loading was primary source of P into the lake. We combined high-frequency in situ measurements of water temperature and dissolved oxygen, discrete grab sampling for nutrient chemistry and remote sensing to provide a comprehensive view the spatiotemporal dynamics of algal blooms in Clear Lake and the potential drivers of the observed variability. Contrary to studies of similar systems, the magnitude of the summer bloom season was correlated to the timing and duration of anoxia rather than the magnitude of spring runoff. By understanding these linkages and the relative contribution of external and internal nutrient loadings interannual variability of bloom severity can be better understood and predicted into the future.