A riparian vegetation simulation module (RVSM) was developed to predict spatially-explicit seed germination, seedling establishment, plant growth and mortality in response to riverine hydrological conditions. The RVSM was integrated into a hydraulic model HEC-RAS and a simplified groundwater model for simulating the interactions between flow and riparian vegetation. The HEC-RAS – RVSM system was applied to the Sacramento River reach to evaluate its capability. River hydraulics, groundwater level and five vegetation types of the study reach were simulated for an 8-year period from 1999 to 2007. The HEC-RAS flow and groundwater were calibrated using observed river stage and groundwater level data at two sites in 2005. Cottonwood seedling density and elevation collected at point bars of River mile (RM) 192.5 and RM183 in 2005 and 2006 were used to calibrate key parameters of vegetation simulation. Two sets of vegetation mapping dated in 1999 and 2007 were used to assign initial conditions and to evaluate the performance of vegetation model. Model results demonstrate that the HEC-RAS – RVSM system successfully reproduced the vegetation area increase of cottonwood, riparian shrub, invasive species and grass as well as the area decrease in mixed forest over the 8-year period.