Three new species of the cyclopoid copepod Halicyclops are described from river estuaries of Ariake Bay, Japan. H. continentalis sp. nov. is most similar to H. laminifer, but differs by the shape of a angular protuberance on the genital double-somite and a serrate hyaline frill of the fourth urosomite. H. sinensis described by Tai and Chen is widely distributed in China and is identifiable to H. continentalis, indicating the population in Ariake Bay is likely a continental relict. H. uncus sp. nov., belonging to the thermophilus group, is distinguishable by the shape of the lateral process on the genital double-somite, a frill of the fourth urosomite, and caudal rami; it is probably endemic to Japan. H. ariakensis sp. nov. differs from the other congeners by a combination of the shape of the prosome, urosomal hyaline frills, and caudal ramus length; it is considered endemic to Ariake Bay.