Estuaries are ecologically vulnerable water bodies and highly affected by pollutants from anthropogenic activities. Excessive nutrient input can cause water eutrophication and deterioration of vital marine ecosystems. However, few studies have compared nutrient salt concentrations and water eutrophication in the Oujiang River Estuary between seasons and their spatial distributions. This study used the single-factor standard index and eutrophication index (EI) methods to analyze the spatial and temporal patterns of nutrient salt levels and eutrophication occurrences in the estuary. Water quality monitoring data was obtained for each season of 2017. The dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP) in the surface and bottom water exceeded the Chinese national standard to varying degrees, but that of DIN was significantly higher. The degree of eutrophication was relatively high. The seasonal DIN and DIP concentrations and EI were as follows: autumn > winter > spring > summer. Spatially, the DIN, DIP, and EI distribution exhibited high values in the estuary and coastal areas, whereas lower values were observed in the open sea and distant shores. The variation in the spatio-temporal characteristics is mainly influenced by ocean currents and terrigenous pollution. Our results provide scientific data support for strengthening environmental protection and sustainable utilization of important water bodies in the Oujiang River and Dongtou Islands.