Harmful algal blooms caused by raphidophyte species of the genus Chattonella (i.e. Chattonella antiqua, Chattonella marina and Chattonella ovata) have been documented in temperate coastal regions around the world. To understand the effects of physicochemical factors on bloom development of Chattonella spp., we investigated the variations of vegetative and resting cells (i.e. cysts) of Chattonella spp. and environmental variables in two coastal environments, Uranouchi Inlet (extremely closed) and Nomi Inlet (semi-closed), with contrasting enclosed natures. Although the vegetative cells and cysts of Chattonella spp. were distributed in both coastal regions, the densities were remarkably higher in Uranouchi Inlet than in Nomi Inlet. The mud content in the sediments of Uranouchi Inlet was also higher than that in the sediments of Nomi Inlet, meaning that fine particles such as cysts are likely to accumulate in the former region. Because of the extremely closed nature of Uranouchi Inlet, warm oceanic waters of the Kuroshio Current penetrate the inlet only infrequently. These results suggest that the closed nature of coastal regions is an important factor influencing either water exchange or the resultant accumulation of Chattonella cells in coastal environments.