This research improves the 3D hydrodynamic model Environmental Fluid Dynamics Code (EFDC), to better capture thermal behaviors in Lake Ontario. Lake Ontario, being in temperate Great Lakes region, exhibits special thermal characteristics including thermal bar evolution in spring and thermal stratification patterns in summer. The thermal bar is a vertical wall of dense sinking water at the temperature of maximum density (4°C), which reduces horizontal mixing, inhibits the exchange of nutrients, and may intensify eutrophication in near-shore areas. During the summer months, the thermal bar disappears, and the lake becomes stratified. Summer temperature differences establish strong vertical density gradients (thermocline) between the epilimnion and hypolimnion, which serve as an energy barrier to vertical mixing Evolution of the spring thermal bar and summer stratification patterns through Lake Ontario is simulated using EFDC. The model is forced with the hourly meteorological data from weather stations around the lake and flow data for the Niagara and St. Lawrence Rivers. The lake bathymetry is interpolated on a curvilinear grid (cells are ~ 2 km2 ) with 20 vertical sigma layers. The simulation is performed from early April to mid-October 2011. The model is improved by (a) updating the evaporation algorithm following Quinn (1979) and Croley (1989) to ensure accurate simulation of evaporation rates and latent heat fluxes (b) specifying appropriate solar radiation attenuation coefficients to ensure sufficient absorption of incoming solar radiation by the water column (c) updating the vertical mixing scheme following eddy diffusivity parameterization by Vinçon-Leite et al. (2014) and eddy viscosity parameterization by Pacanowski and Philander (1981) to better capture thermal stratification. In addition, values for horizontal mixing coefficients, bed heat flux parameters are specified through the model calibration process, and convective velocity mixing is implemented to thoroughly mix the water column from late August. The improved EFDC model simulates overall surface temperature profiles with RMSEs between 1.5-2.5°C. The vertical temperature profiles during the lake mixed phase (early April to late May) are captured with RMSEs < 0.5°C, and the evolution of the thermal bar is replicated. With the newly implemented vertical mixing parameterization, the model captures the summer thermal stratification and thermocline formation from late May to mid-October. The simulated temperature profiles match the observed profiles for a deep (180 m) location, with RMSEs between 0.6 – 1.6 0C. The model captures the thermocline formation at a shallow (19 m) location, with RMSEs of 1.25-3.7°C. The model is further augmented with meteorological data from the North American Regional Reanalysis (NARR) climate model. Simulated vertical profiles at the deep location, and surface temperature profiles using NARR over-lake data match observed data better than the simulations forced by land station based data. This comparative study establishes a baseline for the future coupling of EFDC Lake Ontario model with a regional climate model.