In this study, the heavy precipitation event on 01 December 2015 over Chennai located on the southeast coast of India was simulated using the Weather Research and Forecast (WRF) model. A series of simulations were conducted using explicit convection and varying the planetary boundary layer (PBL) parameterization schemes. The model results were compared with available surface, satellite and Doppler Weather Radar observations. Simulations indicate strong, sustained moist convection associated with development of a mesoscale upper air cyclonic circulation, during the passage of a synoptic scale low-pressure trough caused heavy rainfall over Chennai and its surroundings. Results suggest that veering of wind with height associated with strong wind shear in the layer 800–400 hPa together with dry air advection facilitated development of instability and initiation of convection. The 1-km domain using explicit convection improved the prediction of rainfall intensity of about 450 mm and its distribution. The PBL physics strongly influenced the rainfall prediction by changing the location of upper air circulation, energy transport, moisture convergence and intensity of convection in the schemes YSU, MYJ and MYNN. All the simulations underestimated the first spell of the heavy rainfall. While YSU and MYJ schemes grossly underestimated the rainfall and dislocated the area of maximum rainfall, the higher order MYNN scheme simulated the rainfall pattern in better agreement with observations. The MYNN showed lesser mixing and simulated more humid boundary layer, higher convective available potential energy (CAPE) and stronger winds at mid-troposphere than did the other schemes. The MYNN also realistically simulated the location of upper air cyclonic flow and various dynamic and thermodynamic features. Consequently it simulated stronger moisture convergence and higher precipitation.