Water-based transportation systems are thus very attractive, and autonomy makes such systems economically more viable. In this paper we focus on a potential case of autonomous water-taxis in Bergen, Norway. First, we identify the major operational differences, from a logistics perspective, between conventional manned water-taxis and autonomous ones. Then a mixed integer linear programming model is developed to tackle the facility location, fleet allocation and routing decisions in the daily operations of a water-taxi business. The model in this paper is used to analyse the problem, rather than designed for direct use during implementation. In the computational study, different cases with either conventional or autonomous water-taxis are tested. The results show that autonomy can lead to substantial savings on travelled distance due to number and locations of parking terminals being feasible only for autonomous systems.