A quantitative description of a long-term series of aquatic environmental factors and their spatial distributions was generated using measured data from the Jiaojiang Estuary from 1982 to 2011. The aquatic environmental factors included suspended matter, salinity, and nutrients. Based on these factors, the aquatic ecosystem health in the Jiaojiang Estuary over the last 30 years was analyzed. The results indicated that the suspended matter concentration in the estuary was mainly affected by the amounts of suspended sediment and solid waste, with the value fluctuating over a long period, and the range of high concentration expanded continually;the salinity was mainly affected by precipitation and surface water resources, showing an overall decreasing trend, and the region with low salinity moved seaward and toward the reclamation areas;and the nutritional status, mainly affected by discharge of industrial wastewater and domestic sewage, was satisfactory in the 1980s and 1990s, but the status became severe in recent years. Reclamation had a great influence on these three factors: high reclamation strength led to a significant increase in the suspended matter concentration and a deterioration of the nutritional status, and the reclamation rate was negatively related with the salinity in the estuary. There was a significant positive correlation between the health status of the aquatic ecosystem and salinity, with a correlation coefficient of 0.93. The correlation coefficient between the health status and nutritional status was ?0.71, while the correlation between the suspended matter concentration and health status was not as significant as that of the other two factors. The dynamics of the aquatic environment could be divided into four stages: sustainable health from the 1980s to the 1990s, continued deterioration from 2000 to 2003, improvement from 2004 to 2005, and secondary deterioration from 2006 to 2011. The Jiaojiang Estuary is faced with imminent environmental pressure at present.