Severe thunderstorms are often accompanied by strong vertical air currents, temporary wind gusts, and heavy rainfall. The development of this atmospheric phenomenon over tropical shallow water zones, such as bays, can lead to intensification of atmospheric disturbances and produce a small-scale storm surge. Here, the storm surge that occurred on 19 March 2017 in the Persian Gulf coastal area has been investigated. Air temperature, precipitation, mean sea level pres-sure, wave height, wind direction, wind speed, geopotential height, zonal components, meridional winds, vertical velocity, relative humidity, and specific humidity obtained from the European Centre for Medium-Range Weather Forecasts (ECMWF) and Global Forecast System (FNL) were used to implement the Weather Research and Forecasting (WRF) model. The results showed that the main cause of the storm surge was the occurrence of a supercell thunderstorm over the Persian Gulf. The formation of this destructive phenomenon resulted from a downburst under Cumulonimbus cloud and high-velocity air subsidence, after collision with the sea surface coinciding with the high tide. This caused a severe, yet temporary, gust, which in turn caused the creation of the four waves of 3.1 m height along the coast of Bandar Dayyer.