The concentration of human activities in coastal cities results in the increase of nutrient salts released into the coastal environment and is identified as a major environmental problem for coastal zone management. Large amounts of nitrogen and phosphorus are transported by rainwater-runoff from urban catchments to coastal zones during episodic rainfall events inducing eutrophication problems and increasing the risk of red tide occurrence. This study used a coupled model based on the Storm Water Management Model (SWMM) and Environment Fluid Dynamic Code (EFDC) to simulate the rainfall-runoff pollution load and its effects on eutrophication in Shenzhen Bay, southern China. A storm event of 2014 was used to build the modeling scenarios and thus analyzed the spatial-temporal variation of the rainfall-runoff pollution. The results indicated that: (i) rainfall-runoff pollution loads accounted for 60–80% of the total pollution loads, and rainfall-runoff pollution can result in a short-term impact pollution load on the receiving seawater body; (ii) the transportation of nutrient salts in the coastal zone and the nutrient salts absorbing process by algae are at different times, which suggests urban rainfall-runoff pollution has evidently an effect on variation of the concentration of chlorophyll-A in the bay, and with increasing distance to the city, the seawater body is gradually less affected by rainfall-runoff pollution.