Abstract: This experiment aims to establish a correction method to study salt effect of ammonia in estuarine water with flow injection spectrophotometry. The experiment result suggests that salt effect is largely contributed by Ca2+ and Mg2+ in the solution . In low salt concentration (salinity from 0 to 10),correction coefficient decreased rapidly with increase in salinity;in high salt concentration (salinity from 10 to 30),correction coefficient increased slowly with increase in salinity. Linearity range of ammonia was found in the range of 3.00-300 μg·L-1 with detection limit (3S/N) of 1.97 μg·L-1. Precision of the method was tested at the concentration level of 20.0 μg·L-1 ammonia standard solution for 7 determination,value of RSD found was 4.5%. Test for recovery was performed by standard addition method,giving values of recovery in the range of 80.7%-108%.