In recent years, Mobility as a Service (MaaS) has been discussed to provide new transportation technology services with GIS, IoT, and automated driving technology. In waterfront areas, autonomous water buses and taxies have been developed to integrate land transportation services, such as trains, buses, and taxies. As well as autonomous vehicles and trains, autonomous ships require precise 3D maps and position data obtained by GNSS positioning. Therefore, we focus on 3D measurement with laser scanning and PPP-RTK with QZSS CLAS (centimeter-level augmentation service) to improve the accuracy and performance of GNSS positioning. However, rivers in urban areas, especially in Tokyo, have poor GNSS positioning environments such as places under bridges and highways. Thus, we also focus on Simultaneous Localization and Mapping (SLAM) using laser scanners as a self-positioning approach to achieve indoor-outdoor seamless positioning. In this study, we experimented with 3D river mapping for autonomous ships. We used two laser scanners and a multi-frequency GNSS receiver mounted on a quick charging plug-in electric boat. We selected two rivers as our study areas. The first is Kanda-gawa river as a typical river in Tokyo. The second is Nihonbashi-gawa river as a GNSS-denied environment. In this paper, we present the results of our preliminary experiments.