Kochi, the financial, commercial, and industrial capital of Kerala, can proudly boast a rich legacy of inland water transport, a tradition that dates back centuries. The large network of backwaters, canals, and rivers that crisscross the region has long been the lifeblood of Kochi's economy, facilitating the movement of goods and people with remarkable efficiency. Even today, while modern infrastructure has supplemented traditional modes of transport, the efforts to preserve and enhance its inland water transport system reflect a commitment to the sustainable development of the city. The present paper investigates the satisfaction level of commuters in five key waterway routes, operated by the State Government owned State Water Transport Department (SWTD), and a ferry route operated by Kochi Corporation. A questionnaire survey was conducted among the boat users to gather socio-demographic data, activity and trip characteristics, user satisfaction, and attitude and behavior toward various factors affecting boat operation. The data revealing passengers’ satisfaction level with the waterway operation was also collected. Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA) are used to uncover key service attributes and latent factors influencing service quality across these routes. Importance-performance analysis (IPA) was conducted to identify the relevance and performance of service parameters and thereby the areas requiring improvement in each route, which also offers insights into user satisfaction and potential enhancements needed. This study provides actionable recommendations for policymakers and transportation authorities to enhance water transportation services in Kochi, making them more efficient and user-friendly for commuters.