Gape size limitation and hypoxia tolerance were examined to evaluate the potential of size and physiological (low dissolved oxygen [DO]) refuges for prey in the macrophyte zones of a predator, largemouth bass Micropterus salmoides, and prey, round crucian carp Carassius auratus grandoculis, based on previous studies. The physiological refuge was observed to be more effective than the size refuge for any combination of predator-prey body sizes examined. In case of a 10 g largemouth bass, a size refuge could protect only an approximately 3.5 g round crucian carp, whereas a physiological refuge protected a 0.01 g fish. Field observations revealed a DO gradient that was low near shore and high towards the offshore open area. The threshold DO values for hypoxia tolerance of the two species were substituted and the thickness of the potential physiological refuge was estimated as >3.5 m at day and >12 m at night. The physiological refuge was thicker in the combination of larger round crucian carp and smaller largemouth bass. Hypoxic conditions enhanced the total effect of a macrophyte refuge and play an indispensable role in maintaining local populations of prey species when they inhabit the macrophyte zone with small predators which can invade into the inner part of the zone.