The runoff of the Jiulong River (JLR) is a key parameter that affects the estimation of pollutant flux into Xiamen Bay (XMB). The precise runoff estimation of the JLR can be used to determine the accuracy of the pollutant flux estimation flowing into XMB. In this study, to analyze the hydrological dynamic characteristics and identify the correlation between fixed-site real-time ocean current observations and cross-sectional navigation flow observations, we conducted six navigation observations on two cross-sections of the JLR estuary during the spring tide and neap tide in the normal season, wet season, and dry season in 2020. Simultaneously, we measured hydrological observation data by a fixed-site buoy located in the JLR estuary and collected runoff data that were measured upstream of the JLR. The results showed that the average correlation coefficient between the average velocity of the fixed-point buoy and average velocity of the section was more than 0.90, higher than expected, the minimum average deviation was 4%, and the minimum sample standard error was 5.7%, which was a good result. In this study, we constructed a model for estimating the runoff of the JLR into the sea. The findings demonstrated that Acoustic Doppler Current Profiler (ADCP) online monitoring data were useful to estimate runoff of the JLR with high accuracy, could promote the accuracy of estimated pollutant flux of the JLR's discharge into XMB, and could provide more scientific and reliable basic data for future load flux estimation research.