The establishment periods of switchgrass and Miscanthus can be a time window when evapotranspiration, surface runoff generation, and sediment and nutrients losses are quite different from when the grasses become fully established, and this period may result in environmental concerns for large-scale biomass production. The current SWAT model does not simulate the establishment periods of perennial grasses. In this study, we modified the model to simulate these periods by updating the maximum annual leaf area index (LAI) instead of using a static value in the unmodified model. The improved SWAT model provided more realistic simulations of LAI values and yields comparable to observed yields from field plots during the establishment periods of the two perennial grasses. The modification made in the present study enabled the SWAT model to be more suitable for evaluating perennial biomass grass-related scenarios. © 2017 American Society of Agricultural and Biological Engineers.