The monitoring of Global Aquatic Land Cover (GALC) plays an essential role in protecting and restoring water-related ecosystems. Although many GALC datasets have been created before, a uniform and comprehensive GALC dataset is lacking to meet multiple user needs. This study aims to assess the effectiveness of using existing global datasets to develop a comprehensive and user-oriented GALC database and identify the gaps of current datasets in GALC mapping. Eight global datasets were reframed to construct a three-level (i.e., from general to detailed) prototype database for 2015, conforming with the United Nations Land Cover Classification System (LCCS)-based GALC characterization framework. An independent validation was done, and the overall results show some limitations of current datasets in comprehensive GALC mapping. The Level-1 map had considerable commission errors in delineating the general GALC distribution. The Level-2 maps were good at characterizing permanently flooded areas and natural aquatic types, while accuracies were poor in the mapping of temporarily flooded and waterlogged areas as well as artificial aquatic types; vegetated aquatic areas were also underestimated. The Level-3 maps were not sufficient in characterizing the detailed life form types (e.g., trees, shrubs) for aquatic land cover. However, the prototype GALC database is flexible to derive user-specific maps and has important values to aquatic ecosystem management. With the evolving earth observation opportunities, limitations in the current GALC characterization can be addressed in the future.