In recent years, floating debris in the sea has damaged the environment and harmed wildlife. Systems for collecting floating marine debris in the open ocean by installing a huge net or using a vacuum device have been proposed. However, to the best of our knowledge, there is no system for collecting marine debris in complex topographies, such as ports wherein marine debris tends to accumulate, and large vessels cannot enter. This study proposes a system to locate and collect floating marine debris by jointly using an unmanned aerial vehicle (UAV) and an unmanned underwater vehicle (UUV). The UAV discovers marine debris that cannot be observed by the UUV owing to its limited view, and the UUV is used for collection. However, for application of such a system, problems related to target detection, UUV navigation, and target collection must be solved. In the proposed system, the following components are developed: a graphical user interface to select the collection target, controller for the UUV to navigate to the target, and a collecting motion generator. We tested and evaluated the proposed cooperative system using a dynamic simulator and physical robots. As a result, we confirm that our system can achieve efficient debris collection in complex topographies, is easy to use, will reduced workload, and can be applied practically.INDEX TERMS Aerial view, cooperative system, marine debris cleaning, multi-view, teleoperation.