Estuary is a key area of the land-ocean interaction zone with important ecosystem services. It had received more and more nutrients from watersheds and other sources due to rapid economic development, leading to a significant increase in eutrophication potential. In this study, the Index of Coastal Eutrophication Potential (ICEP) was used to quantify the impacts of riverine inputs in the Jiulong River Estuary, particularly focusing on analyzing the annual and seasonal dynamics of ICEPs. The results showed that the annual average dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP) concentrations remarkably increased with large fluctuation. Nutrient loads in the Jiulong River Estuary had significantly altered since the 1980s, with a mean DIN flux of 3.967×10³ t/a during 1981-2006 and 2.924×10⁴ t/a during 2006-2020, respectively. The DIN fluxes during 2006-2020 increased 637.14% compared to the previous period (1981-2006), with a peak flux of 8.279×10⁴ t/a. The annual mean DIP fluxes in the same two periods were 1.131×10² t/a and 2.282×10² t/a, respectively, with an increasing rate of 101.87% and the highest flux of 6.128×10² t/a. The riverine nutrient fluxes and their structure in the estuary were significantly altered. After 2006, the N-ICEPs became positive for 90% of the years, while the P-ICEPs were negative throughout all years. Seasonal variation showed the ICEPs were low in Winter, but high in Summer. The chlorophyll-a concentrations were significantly correlated with both N-ICEPs and P-ICEPs. However, diatom abundance was negatively correlated with both N-ICEPs and P-ICEPs. The contribution of the P-ICEPs to chlorophyll-a concentrations was higher than that of the N-ICEPs in the estuary, suggesting primary productivity of the estuary was generally phosphorus-limited, but with dual limitation by P and Si in both summer and autumn. Therefore, seasonal variation is essentially taken into account when dealing with the eutrophication problem. Since ICEP directly reflects changes in stoichiometric ratios of N, P, Si and ecological consequence, it is a powerful management tool in estuaries for future sustainable development goals.