Yellow perch (Perca flavescens; YP) is an economically and ecologically important species across the Great Lakes, which demonstrates variable recruitment to the fishery that we hypothesize is regulated by physical processes operating during early life stages. For example, Ludsin et al.’s GLFC-sponsored YP-River Discharge project has shown that Lake Erie YP recruitment success is positively correlated with Maumee River inflow and plume size during spring. However, uncertainty in predicting the distribution of these attributes, as well as their effect on movement, predation risk, consumption, growth, and survival of YP larvae in dynamic, shallow waters remains a major impediment to fully understanding and forecasting recruitment to the fishery in this system. We built a coupled biophysical model to better understand and predict YP foraging, growth, survival, and recruitment in western Lake Erie. It is widely known that nearshore and coastal water is the important region in Great Lakes and ocean and it has complex geometry of coastline, a high-resolution unstructured grid model is required for the nearshore region. So an extant three-dimensional, wave-current, coupled Finite Volume Coastal Ocean Model (FVCOM) was used to simulate water movement in Lake Erie, particularly the western Lake Erie and its tributaries. In this study, we also present the improved water quality model and their application to Lake Erie. We will evaluate the interactive effects of river discharge and wind-driven currents on the plume and nutrient, phytoplankton and zooplankton distribution which are important to the creation and expansion of high-quality nursery habitat. The Erie model is also coupled with wave model or FVCOM-SWAVE to simulate the effect of waves on nearshore circulation and velocity fluctuations. The effect of wave to the nutrient/zooplankton dynamics is further investigated. We also calibrate and validate the model using physical (e.g., temperature, water clarity, currents) and biological (e.g., zooplankton, nutrient) data collected in western Lake Erie via prior GLFC-sponsored research and agencies (e.g., ODNR, OMNR). Overall, we found the Erie bio-physical simulation is highly sensitive to the model grid resolution; the circulation is highly sensitive to the boundary condition types; and wave is very critical to the circulation pattern, particularly under some episodes. This model will be linked to a model of larval YP movement, foraging, growth, and survival. Few studies have been conducted to explore how physical factors influence transport and survival of fish larvae in nearshore environments of the Great Lakes. We will be using the model to test hypotheses about the influence of physical factors on larval YP transport and recruitment success by analyzing patterns of fish larvae transport, growth, and survival under various conditions, including seasonal river floods, strong wind-induced wave conditions, and fluctuating prey fields. Thus, our research will shed insight into how lake physics influence fish distributions, survival rates, and population dynamics in Lake Erie and other similar water bodies in the future.