Water pollution generated by accidental spill of hazardous materials is a growing problem worldwide.There is an urging need for a tool which would help environmental response teams to perform rapid understanding of the location and the extent of the spill, to effectively establish an appropriate response. This paper presents a cooperative robotic system for environmental monitoring consisting of an Autonomous Underwater Vehicle (AUV) and an Autonomous Unmanned Surface Vehicle (USV). The main contributions of the paper are: systematic description of the design and implementation of the proposed cooperative robotic system, novel human-on-the-loop (HOTL) approach applied on the system for environmental monitoring and demonstration of the results of the open-sea experiments on pollution deliberately caused by harmless Rhodamine WT, carried out in Cartagena, Spain in June 2015. The proposed HOTL system provides near real-time pollution measurement data, while not consuming a significant amount of human time and effort. It supports decision-making and allows the operator to initiate the most adequate mission in a current situation, i.e., ensures mission change on-the-fly. While the AUV samples the ocean, the USV maintains the localization and communication data transfer to the control centre and corrects the AUV’s dead reckoning error.