The zoanthid, Palythoa caribaeorum, is a good indicator of coral bleaching because it is highly susceptible to bleaching under physiological stresses. We show that water flow accounts for variation in thermal bleaching sensitivity of P. caribaeorum within and between colonies. Sample colonies were exposed to two flow regimes (low = 3 cm s− 1; high = 15 cm s− 1) and two temperature regimes (low = 26.5 °C; high = 33.5 °C) in a unidirectional flume for 48 h. Six individual colonies of two sizes (small = 2.3 ± 0.2 cm; large = 7.3 ± 0.4 cm in diameter) were tested per flow regime. Degrees of bleaching were measured by zooxanthellae count and chlorophyll a concentration. Bleaching of P. caribaeorum was induced by high temperature. High water flow mitigated bleaching, but there was considerable variation in bleaching within and between colonies. Upstream sides of large colonies bleached less than downstream sides in high flow. High water flow also moderated bleaching of small colonies more than large colonies. One possible explanation for these results is that high mass transfer rates mitigate bleaching. This may be more easily accomplished in small colonies, in which the entire colony tends to be exposed to high water flow; thus, small colonies have an advantage during bleaching events.