In order to study the influence of the tank environment on the results of the seaplane model test, for the first time in this field, a series of whole aircraft model tests were conducted using the same seaplane model in two towing tanks to study the aerodynamic and hydrodynamic characteristics of the whole aircraft model in the two towing tanks, the test results and environmental differences were analyzed. The results show that the towing tank environment has a significant impact on the aerodynamic characteristics of the seaplane model, but by compensating the aerodynamic characteristics of the seaplane model in each towing tank during the test, the interference of the test environment on the water resistance results could be avoided, so as to obtain a more satisfactory water resistance test result. Among the boundary effects of the towing tank, the blockage effect has the greatest impact on the aerodynamic characteristics of the seaplane model. Compared with 2.51% relative blockage ratio 0.67%, the aerodynamic drag coefficient of the seaplane model is 0.1 ~ 0.2 larger, and the lift coefficient is at least 0.2. Because the typical high-speed coasting state is used for aerodynamic compensation to calculate, so the compensation effect is only achieved at the corresponding speed and produce some deviation at other speeds, resulting in a certain deviation in the test result, but it will not have a significant impact on the test result because the deviation is so small. The research findings provide guidance for model hydrodynamic tests and performance analysis of seaplanes in China.