Chinese coastal waters support vast fisheries and vital economies, but their productivity is threatened by increasingly frequent harmful algal blooms (HABs). Here we provide direct experimental evidence that atmospheric deposition, along with riverine input, opens new niches for bloom-forming dinoflagellates and diatoms in the East China Sea (ECS) by increasing the ratio of nitrogen to phosphorus (N:P), inducing severe P limitation, and altering trace metal micronutrient inventories.