Anthropogenic processes associated with eutrophication can make the coastal marine ecosystem of Manila Bay to be more susceptible to ecological perturbations including harmful algal blooms (HABs). The spatial and temporal expansion and increased intensity of HABs is a globally recognized phenomenon and this expansion has already been observed in Manila Bay where HABs have become a human health, economic and environmental threat. Manila Bay experiences at least two distinctive types and detrimental impacts of HABs annually since 1988, which are: (1) toxins producing-algae causing variety of illnesses in humans due to consumption of contaminated shellfish and/or fish, and (2) mono-species blooms or “fish killer” red tide directly causing fishery economic losses due to massive kills of shellfish and fish from both aquaculture farms and natural environment. This paper provides important information regarding each of these HABs including local historical accounts of each type of HABs, their causative phytoplankton species, and impacts as basis for urgent management measures required to mitigate deteriorating coastal water quality and to reduce if not totally eliminate their occurrences in Manila Bay.