Iron (Fe) is a crucial trace element in marine ecosystems, playing a vital role in regulating marine primary productivity and driving marine biogeochemical cycling processes. However, understanding seasonal iron variations and the response of chlorophyll-a (Chl-a) to coastal waters remains limited. The aim of this study was to find out about the spatial and seasonal variations in iron concentrations and their impact on chlorophyll-a levels in Zhanjiang Bay. We conducted seasonal monitoring of surface seawater for iron in 2019, alongside assessments of terrestrial iron inputs during three precipitation seasons. The monitoring results showed that the iron content in Zhanjiang Bay ranged from 0.83 to 339.2 μg·L−1 with an average of 54.34 ± 75.91 μg·L−1. The annual average iron content in the central bay is higher than that in the bay mouth and inner bay. The iron content in autumn is much higher than that in other seasons, which may be due to the influence of river dredging. Correlation analysis revealed that temperature and pH are the main factors affecting the iron content in Zhanjiang Bay and the spatial distribution of iron is influenced by rainfall, river inputs, and human activities, particularly channel dredging. Iron content and chlorophyll-a were negatively correlated between different seasons, which was more significant with the increase in iron content. This may mean that the increase in iron concentration may inhibit the synthesis of chlorophyll-a, thus affecting primary productivity. We need to carry out more research experiments to verify this hypothesis. This study reveals the spatial and temporal changes in iron in urban coastal waters and its relationship with environmental factors, which is of great significance for understanding the marine biogeochemical cycle of iron in coastal eutrophic waters and specifying effective environmental management strategies.