The geographical conditions of Colombia limit connectivity among regions, making communication between different areas of the country difficult. Although Colombia has a major waterway system that could facilitate regional communication, much of the territory is functionally disjointed, which is why the government and private operators seek to promote inland waterway transport and improve their safety. In the field of provision of waterway transport in inaccessible regions, this paper analyses the influence that perceptions of safety and comfort of the service have on the choice of river transport by passengers using hybrid choice models incorporating latent variables. The results of the hybrid choice model indicate that older workers attach less importance to the hull condition and safety; in turn, comfort is more valued by young workers and by those users who have a higher educational level. Variables such as the hull condition and how the boat is operated have a significant effect on the user perception of safety. Similarly, the results suggest that expanding the space between seats and developing strategies to improve the behaviour of other users significantly increase the perceived comfort of the service provided.