Waterway intersections pose significant risks for vessel navigation due to the complexities of operational conditions in these areas. The lack of clear collision avoidance rules, combined with ineffective communication, exacerbates these dangers. To address this issue, transportation authorities will typically employ flow organization strategies to optimize operations at these intersections. However, effective methods for traffic management, both before and after implementation, are still lacking. This paper proposes a methodology to determine the level of service (LOS) needed for waterway intersections by using the degree of conflict during vessel navigation as a performance measure, while also considering the unique characteristics of vessel encounters in these areas. The methodology was applied to analyze the Yuxingnao waterway, and the results demonstrate its effectiveness in assessing operational conditions and providing a clear classification of service levels over specific time periods. Consequently, this methodology not only enables transportation authorities to evaluate the effectiveness of traffic management strategies, such as route planning and traffic organization, but also helps predict the impact of potential improvement countermeasures.