ABSTRACT: Larvae of many benthic marine animals settle and metamorphose in response to waterborne chemical cues. Can the behavioral responses of microscopic larvae in the water column to dissolved chemical cues affect their transport to the substratum in the turbulent, wave-driven flow characteristic of many shallow coastal habitats? We addressed this question using an individual-based model of larvae of the sea slug Phestilla sibogae, transported in the oscillatory flow above coral reefs. Larvae of P. sibogae stop swimming and sink in response to a dissolved inducer released by their prey, the coral Porites compressa, and resume swimming when exposed to inducer-free water. The instantaneous fine-scale spatial distribution of inducer in the flow above a reef is filamentous; hence microscopic larvae swimming or sinking through the water encounter inducer above threshold concentration in on/off temporal patterns. Model results show that using a time-averaged inducer concentration gradient to calculate larval transport rates to the reef overestimates the rates by <15% (depending on the threshold concentration of inducer required to trigger larval sinking) compared with those calculated using time-varying, fine-scale inducer distributions. Aspects of larval behavior that have large effects on rates of transport to the substratum are swimming speed and direction, sinking speed, and sensitivity (threshold concentration) and responsivity (percent of encounters eliciting a response) to inducer. In contrast, lag times to start sinking after encountering inducer or to resume swimming after re-entering inducer-free water, have negligible effect.