Algal blooms have been identified as one major threat to coastal safety and marine ecosystem functioning, but the dominant mechanism regulating the formation of algal blooms remains controversial, ranging from physical control (via water column stability), the chemical control (via coastal nutrients) to joint control. Here we leveraged the unique data collected in the Hong Kong water over the annual cycle and past three decades, including direct observations of algal blooms and coastal nutrients and process model output of water column stability, and evaluated the differential competing hypotheses in regulating algal blooms. Our results demonstrate that the joint mechanism rather than the single mechanism effectively predicts all algal blooms. Meanwhile, we observed that the adequate nutrients (phosphate, PO) significantly originate from coastal groundwater. The production and fluctuation of PO in beach aquifers are primarily governed by groundwater temperature, leading to a sustained and sufficient supply of PO in a low groundwater temperature environment. Furthermore, along with submarine groundwater discharge (SGD), the ongoing release of PO in groundwater enters coastal waters and serves as sufficient nourishment for promoting algal blooms in coastal areas. These results highlight the importance of both physical and chemical mechanisms, as well as SGD, in regulating coastal algal blooms. These findings have practical implications for the prevention of coastal algal blooms and provide insights into mariculture, water security, and the sustainability of coastal ecosystems.