While storm water runoff and surface loading of nutrients into the lower St. Johns River (LSJR), Florida have been explored in great detail, the groundwater discharge of nutrients into the river has not yet been thoroughly quantified. A field estimation of shallow groundwater discharge and nutrient load from the selected sites into the adjacent LSJR was performed in this study. The groundwater discharges were obtained by using Darcy's law along with the hydrological parameters collected from our study. Based on groundwater discharges and nutrient concentrations, groundwater nutrient loads into the river were then estimated. In general, seasonal groundwater level variations were larger than those of the river stage, whereas site variations of groundwater nutrient concentrations were larger than seasonal variations of groundwater nutrient concentrations. The average groundwater discharge rate was about 0.012 m3/m2/d and the average groundwater nutrient loads into the adjacent river were estimated to be 10.6, 11.0, and 5.6 mg/m2/d, respectively, for NOx, TN and TP. This information is useful for establishment of pollution reduction loads (PLRGs) and development of total maximum daily loads (TMDLs).