Previous research results indicated that dry weather condition has complicated impacts on nitrogen dynamics; monitored and modeling data showed both increased and decreased levels. In order to facilitate the total maximum daily loads (TMDLs) development at three tributaries of St. Louis Bay estuary, the nitrogen dynamics were investigated for two designed critical flow conditions by integrating Hydrological Simulation Program Fortran (HSPF), Environmental Fluid Dynamics Code (EFDC), and Water Quality Analysis Simulation Program (WASP). The total amount of precipitation during the dry year corresponded to a flow condition with return period of 50 years, and 10-year return period for wet year. The dry year contributed more total nitrogen (TN) loads per unit flow volume. At the upstream tributaries, the computed peak reach-averaged TN concentrations were significantly higher for dry weather simulation than wet conditions, whereas at the near-bay tributary, there were no significant differences in the peak TN concentrations. Hence, for the upstream tributaries, the nitrogen TMDL calculation should be based on dry weather condition since the decision-makers are more concerned about the worse scenario.