Insights into the dynamics of harmful algal blooms in a tropical estuary through an integrated hydrodynamic-Pyrodinium-shellfish model

•Developed a novel model integrating Pyrodinium, physical, and shellfish dynamics.•Model captured temporal variabilities of Pyrodinium cells and shellfish toxicities.•Even when cysts could excyst, Pyrodinium increased only when rainfall increased.•Pyrodinium decline was affected by shellfish grazing and cell mortality.•Role of cysts in shellfish toxicity could be important and needs to be examined.