Field observations were combined with a coupled hydrodynamic and water quality model to investigate the spatial and temporal variation in Chlorophyll-a (Chl-a) in Jinmeng Bay, China. The relatively high Chl-a values were distributed in the inshore waters, mainly due to the abundant nutrient inflow from the Tanghe River. The model’s results indicate that the Chl-a concentration was much higher in seaweed beds surrounded by artificial islands and reefs under the southeasterly wind, largely due to the fact that pollutants are prone to accumulate in coastal areas where flow is attenuated by the presence of natural and artificial marine structures. It was also found that the southwesterly winds suppress the inflow of nutrients from the Tanghe River to the coastal areas, and, therefore, lower the Chl-a levels. River input and wind forcing are the major factors that influence Chl-a concentrations in the anthropogenically influenced bay. This finding provides useful guidance for the prediction and mitigation of green tides in Jinmeng Bay in the future.