In contrast to temperate Harmful Algal Blooms (HABs), knowledge on the mechanisms driving tropical HABs are less well studied. The interaction of a seasonal temperature window, cysts (for certain species) and large-scale transport are some of the key processes in temperate HABs. In the Philippines, HABs occur not along long open coastlines, but in embayments that are highly influenced by run-off and stratification. These embayments are typically also the sites of cultured or wild harvest shellfish and other aquaculture activities. Sorsogon Bay in the northeastern Philippines has experienced prolonged shellfish-harvesting bans due to blooms by Pyrodinium bahamense var. compressum severely affecting the fisheries industry in this area, as well as leading to Paralytic Shellfish Poisoning illnesses and fatalities. A novel integrated model was developed that mechanistically captures the interactions between hydrodynamic conditions, nutrients, the life history (cells and cysts) of Pyrodinium, as well as the cultured shellfish within the bay and their ensuing toxicities due to ingestion of toxic Pyrodinium cells and cysts. This is the second model developed for HABs in the Philippines, and the first to integrate different components of Pyrodinium bloom dynamics. The model is modularly composed of a watershed nutrient and diffusion model, a 3D hydrodynamic model, a Pyrodinium population model and a shellfish toxin model. It was able to capture the observed temporal variations of Pyrodinium and shellfish toxicity. It was also able to represent some aspects of the spatial distribution in Sorsogon Bay though there were discrepancies. To explore the dynamics of blooms, the linkages between the bloom and decline of the Pyrodinium population with shellfish toxicity as affected by temperature, salinity and nutrients were investigated. Comparisons with field results showed the seasonality of blooms in Sorsogon Bay is driven by increased rainfall. The timing of these conditions is important in facilitating Pyrodinium excystment and reproduction. Model results showed as well the potential significance of shellfish grazing and dinoflagellate cell mortality in influencing the decline of the bloom, and toxicity levels. This approach is promising in helping to understand mechanisms for HABs more holistically, and the model can be further improved to provide more precise quantitative information.