This study investigated eco-tour ships at Nakdong estuary, Suncheon wetland, and Goesan and Sanmagi-yetgil, 3 of the 26 ecotourism sites in Korea, by analyzing the characteristics and level of ecotourist satisfaction. The field investigation focused on eco-tour ship image, facilities, landscape observed from eco-tour ship, course, and operations. The results of the satisfaction analysis can be summarized as follows. First, there was no significant difference in satisfaction of eco-tour ship image between Nakdong estuary and Sanmagi-yetgil (p > 0.01), while Suncheon wetland showed a significant difference (p < 0.01). It is assumed that the fact that the ship was built using timber which better suits the natural environment and coastal ecosystem had a positive impact on the visual image. No significant difference in satisfaction with facilities on eco-tour ships was found between Nakdong estuary and Suncheon wetland, while Sanmagi-yetgil showed a significant difference. Second, satisfaction of the landscape observed from the eco-tour ships showed significant differences in the mean scores of landscape evaluation the three target sites: Sanmagi-yetgil (8.40), Suncheon wetland (7.20), and Nakdong estuary (4.67). These values are based on the qualitative evaluation of the landscape as seen from the eco-tour ship. It is presumed to have been influenced by the diversity of the landscape and the width of the river. The eco-tour ship course satisfaction also showed significant differences in the mean scores: Sanmagi-yetgil (7.37), Suncheon wetland (6.57), and Nakdong estuary (5.00). The landscape and tour course evaluations of the respondents seem to be correlated. In particular, the variety of courses available to visitors in Sanmagi-yetgil was relatively high compared to Nakdong estuary and Suncheon wetland. Third, satisfaction analysis for eco-tour ship operations found that Suncheon wetland and Sanmagi-yetgil did not differ significantly in terms of satisfaction (p = 0.634), but Nakdong estuary showed a significant difference. The relatively low satisfaction with the eco-tour ship operation at Nakdong estuary is due to the low scores for eco-tour ship commentary, reservation system, and with the facilities, while it is shown that the operation time as well as the landscape observed from the eco-tour ship and the tour course had a combined influence on satisfaction. In the comparative analysis of the impact of eco-tour ships on ecotourism, Nakdong estuary showed a significant difference. This finding indicates a greater influence of eco-tour ships on ecotourism in Suncheon wetland, Sanmagi-yetgil, and Nakdong estuary. Enhanced ecotourism satisfaction improves the probability of return visits. Thus, there is a need to incorporate the characteristics of ecological resources with well thought out operation and increased functional suitability of eco-tour ships to improve ecotourism satisfaction. The eco-ships in the three places in this paper have elements promoting and enhancing their potential. Our findings showed the satisfaction level of the users with the theme of ecotourism.