In temperate macroalgal forests, sea urchins are considered as a keystone species due to their grazing ability. Given their potential to shape benthic communities, we monitored the habitat use by three sympatric sea urchin species and compared their behaviors in a vegetated habitat (VH) and an adjacent isoyake habitat (IH). We monitored the environmental conditions and sea urchin density along deep and shallow transects of the VH and IH for over a year. The benthic rugosity at both sites were also surveyed. A mark-recapture experiment was conducted on the two most abundant sea urchins, Diadema setosum and Heliocidaris crassispina, to elucidate sea urchin movement patterns and group dynamics. We found that exposure to waves was highest at the VH while the IH was sheltered. The deep IH experienced the least amount of light due to high turbidity. Water temperature patterns were similar across sites. The VH benthic topography was more rugose compared to the smoother and silt-covered IH substate. Peak macroalgal bloom occurred three months earlier in IH, but macroalgae persisted longer at the shallow VH. Among the sympatric sea urchins, H. crassispina was most abundant at the shallow VH and was observed in pits and crevices. The most abundant across IH and in the deep VH was D. setosum, preferring either crevices or free-living, depending on hydrodynamic conditions. The least abundant species was D. savignyi, and most often observed in crevices. Small and medium sea urchins were most often observed at the IH site, whereas larger sea urchins were more likely observed at the VH. The mark-recapture study showed that D. setosum was found to displace further at the IH, and H. crassispina was more sedentary. Additionally, D. setosum was always observed in groups, whereas H. crassispina was always solitary. The behaviors of sympatric urchins, Diadema savignyi, D. setosum and H. crassispina, differed in response to changes in the benthic environment and physical conditions. Sea urchin displacement increased when rugosity and wave action were low. Habitat preference shifted to crevices in seasons with high wave action. In general, the mark-recapture experiment showed that sea urchins displaced further at night.