Research was conducted on optimizing the seaplane transportation system in Greece using the Choice-Base Conjoint Analysis method. Due to its geographical morphology and its level of touristic development, Greece is considered an ideal country for using seaplanes. A sample of 216 people were asked questions related to the utility of seaplanes, the quality of seaplane services, and seaplanes’ quality characteristics as set mainly by the Greek business world but also by their standards of use from foreign tourist countries in the field of touristic services. The results were the basis for designing scenarios simulated in market conditions. These scenarios were evaluated in comparison to each other regarding their quality characteristics and the scale of their appeal to the public regarding their contribution to a more effective use of seaplanes. It was found that the optimal seaplane transport system is as follows: The seaplane capacity consists of 18 persons, the frequency of the flights is three (3) times per day, no intermediate stop is interposed, the departure times are in the afternoon, and the cost of the ticket is equal to the cost of traveling by car. The attributes were found to have the following importance: (i) ticket cost, 45.13%; (ii) density of the flight, 21.76%; (iii) intermediate stops, 15.61%; (iv) capacity and size of the seaplane, 11.14%; and (v) departure times, 6.35%. This optimal system gathered 77.28% of respondents who prefer it over the base system, with a rate of 22.72%.