Oxygen consumption rates were measured for coral reef fishes during swimming in a bidirectional, oscillatory pattern to simulate station-holding in wave-induced, shallow-water flows. For all species examined, increases in wave intensity, as simulated by increases in frequency and amplitude of oscillation, yielded increased metabolic rates and net costs of swimming (NCOS; swimming metabolic rate minus standard metabolic rate). Comparing species with different swimming modes, the caudal fin swimming Kuhlia spp. (Kuhliidae) and simultaneous pectoral-caudal fin swimming Amphiprion ocellaris (Pomacentridae) turned around to face the direction of swimming most of the time, whereas the median-paired fin (MPF) swimmers, the pectoral fin swimming Ctenochaetus strigosus (Acanthuridae) and dorsal-anal fin swimming Sufflamen bursa (Balistidae), more frequently swam in reverse for one half of the oscillation to avoid turning. Contrary to expectations, the body-caudal fin (BCF) swimming Kuhlia spp. had the lowest overall NCOS in the oscillatory swimming regime compared with the MPF swimmers. However, when examining the effect of increasing frequency of oscillation at similar average velocities, Kuhlia spp. showed a 24% increase in NCOS with a 50% increase in direction changes and accelerations. The two strict MPF swimmers had lower increases on average, suggestive of reduced added costs with increasing frequency of direction changes with this swimming mode. Further studies are needed on the costs of unsteady swimming to determine whether these differences can explain the observed prevalence of fishes using the MPF pectoral fin swimming mode in reef habitats exposed to high, wave-surge-induced water flows.