A size-structured, time and vertically-dependent model was used to investigate the effects of water column structure on the distribution of larvae of the oyster Crassostrea virginica. Formulations used to model larval growth and behavior are based upon laboratory studies. Simulated vertical larval distributions obtained for conditions representative of a well-mixed, partially stratified and strongly stratified water column illustrate the effect that salinity and temperature gradients have on moderating larval swimming and hence on larvae vertical location. For well-mixed conditions, smaller larvae are dispersed throughout most of the water column. For strongly stratified conditions, the smaller-sized larvae cluster within the region of strong salinity change. Intermediate-sized larvae cluster within or directly below the region of strong salinity change. The oldest larvae are found near the bottom for all salinity conditions since their location is determined primarily by sinking rate. Additional simulations show that diurnal salinity changes interact with larval behavioral responses to create patchy larval distributions. Finally, simulations show that the inclusion of an upwelling or downwelling velocity can overwhelm the behavioral responses of smaller larvae and result in much different vertical distributions. The simulated vertical larval distributions show that changes in larval migratory behavior which are brought about by changes in the vertical salinity gradient can significantly alter larval distribution patterns. These, when combined with horizontal advective flows, have important implications for larval dispersal