The aim of the present work was to unravel which environmental drivers govern the dynamics of toxic dinoflagellate abundance as well as their associated paralytic shellfish toxins (PSTs), diarrhetic shellfish toxins (DSTs) and pectenotoxin-2 (PTX2) in Ambon Bay, Eastern Indonesia. Weather, biological and physicochemical parameters were investigated weekly over a 7-month period. Both PSTs and PTX2 were detected at low levels, yet they persisted throughout the research. Meanwhile, DSTs were absent. A strong correlation was found between total particulate PST and Gymnodinium catenatum cell abundance, implying that this species was the main producer of this toxin. PTX2 was positively correlated with Dinophysis miles cell abundance. Vertical mixing, tidal elevation and irradiance attenuation were the main environmental factors that regulated both toxins and cell abundances, while nutrients showed only weak correlations. The present study indicates that dinoflagellate toxins form a potential environmental, economic and health risk in this Eastern Indonesian bay.