Effect of water disturbance on grazing by the sea urchin with the refuge habitat was estimated. We tested the hypothesis that sea urchins ceased feeding and remained in refuge habitat for protection against disturbance even though water flows were not high to inhibit their grazing. Fecal density from sea urchins was positively related to their residence time under the undisturbed condition. This result suggested that the fecal density is a useful criterion for understanding the residence time of sea urchins in the calm condition. Five types of structure (L-shaped, cave shaped, crack-shaped, smaller and larger rectangular structure) as refuge habitats were deployed in the undisturbed tank with sea urchins and the fecal densities at each structure were measured to examine the habitat forms which sea urchins prefer. This experiment indicated that the crack-shaped form was used for sea urchins as the refuge habitat. Feeding rate of sea urchins inversely corresponded to water flow. Feeding rates with the refuge habitat were lower than in the absence of habitat, although water disturbances were almost the same. The presence of refuge habitat seemed to be a factor responsible for the reduction of their grazing, because sea urchins sheltered to avoid water disturbances.