The occurrences of phytoplankton bloom have recently increased in some coastal bays in Indonesia. Harmful algal blooms are now a significant problem for several coastal bays, which causes problems and economic losses to the fishing industry, harm to aquatic ecosystems, fish mortalities, and other living organisms. The negative impact also affects the marine environment, tourism, and consumer health. The most frequent algal bloom occurrences are three coastal bays: Jakarta Bay, Lampung Bay, and Ambon Bay. In particular, those three bays are the most infected areas of harmful algal bloom in this country. Samples were taken using a 20 um net plankton and directly preserved with Lugol’s solution before being identified. Some bloom maker species were identified as toxic, mainly belonging to dinoflagellates, such as Pyrodinium sp, Aleandrium sp, Gymnodinium sp, and Cochlodinium sp. And the species that most frequently cause a bloom in those coastal waters are Skeletonema, Chaetoceros, Trichodesmium, and Noctiluca. The nutrients, mainly nitrate and phosphate, are the main driving factor resulting from anthropogenic activities on the land that make the coastal waters eutrophic. This paper discusses the recent distribution, causes, and impact of harmful algal blooms in the three coastal bays in this country.