This study examined challenges posed by two ferry routes, namely, Likoni and Mtongwe crossings, in the Mombasa Channel and their impact on navigational safety. Utilizing the Environmental Stress (ES) model, this study analyzed current ship traffic and assessed stress levels imposed by ferry crossing traffic on navigators. ES values revealed significant stress at these ferry crossings attributed to varying transit speeds. Standardizing transit speeds at two ferry passages can reduce high stress levels, presenting a viable solution. Furthermore, the IWRAP Mk2 simulation underscores crossing collisions as a significant concern, particularly at Likoni and Mtongwe crossings, due to increased ferry traffic. This research offers valuable insights for stakeholders, such as the Kenya Ports Authority (KPA), to develop targeted safety measures and enhance the flow of ship traffic in the channel.