The research aims to find out the existence and the most dominant rotifera in coastal territorial waters and estuaries in North Sulawesi, and their relationship with temperature, salinity, turbidity, dissolved oxygen, and nutrients. The research was conducted in Manembo-nembo, Minanga, Wori, and Tumpaan. Identification of rotifera revealed three species of rotifera from all locations, i.e. Brachionus rotundiformis, Brachionus caudatus, and Brachionus quadridentatus, with abundance value of 1984.4 ind/m3; 26.1 ind/m3; and 212.9 ind/m3 respectively. Result of analysis indicates that abundance of those three rotifera are significantly different both between locations and sampling sites. The abundance of B. rotundiformis in Manembo-nembo and Minanga is higher compared to those in Wori and Tumpaan. The abundance of B. caudatus is higher in Manembo-nembo and Minanga compared to those in Wori and Tumpaan. The abundance of B. quadridentatus is also different from the other two species, the abundance is sifnificantly different in Minanga compared to those in Manembo-nembo and Tumpaan, but is not significantly different with those from Wori. The highest abundance of B. rotundiformis was found in brackishwater pond and the lowest was in coastal area. Key words: bioecology, rotifera, coastal water, estuary