Environmental conditions on higher latitude coral reefs can be extremely variable, and may structure fish communities in ways not previously observed in the more stable, low latitude locations where communities have usually been studied. Temporal changes in fish community structure were examined in an intensive two-year study of the reef fishes of Hanalei Bay, Kauai, Hawaii. Hanalei Bay is directly exposed to winter swells with high surf, as well as frequent heavy winter rainfall and high river discharge. Twenty-two transects (25 x 5 m) were established in a wide variety of habitats and censused monthly (N = 1052 censuses). Over 121 000 sightings of individuals from 150 species were made during the study. Seasonal patterns in number of species, number of individuals, species diversity, and evenness were observed, with winter values usually lowest. Values of these ensemble variables tended to be higher at deeper sites and at sites with greater habitat complexity. Surf height and degree of wave exposure were negatively correlated with several measures of community organization. Groups of fishes with different levels of spatial mobility tended to occupy depths consistent with their various abilities to respond to events of heavy weather. The rank abundance of fish taxa tended to be more stable seasonally at sites with less exposure to high wave energy. These seasonal effects may suggest some type of short-range movement from more exposed and monotypic habitats to locations that are deeper or otherwise provide refuge from seasonally heavy seas.