The transport of larval yellow perch (Perca flavescens) in Lake Michigan is studied with a 3D particle trajectory model. The model uses 3D currents generated by the Great Lakes version of the Princeton Ocean Model driven by observed momentum and heat fluxes in June-August 1998, 1999 and 2000. Virtual larvae were released in the nearshore region with the most abundant preferred substrate for yellow perch spawning, rocks. We also investigated the potential for physical transport mechanisms to affect recruitment of Lake Michigan yellow perch by coupling hydrodynamic models with individual-based particle models of fish larvae to study variation in larval distributions, growth rates, and potential recruitment. Larval growth rates were simulated using a bioenergetics growth model with fixed consumption rates. Results indicate that lake circulation patterns are critical for understanding interannual variability in Great Lakes fish recruitment.