Monitoring as well as achieving related water quality goals for rivers is a challenge on several scales of both space and time. There are several factors influencing the most effective actions to implement, when it comes to water quality. Collecting water quality data can be challenging and expensive as maintaining specialized equipment can raise costs over time. Within the MultiMonD2 project, a multi-agent platform of micro-laboratories specialized in the water quality monitoring of the Danube river and Delta is being developed. Aerial and surface water vectors are used as carrier systems for sensor-based detection equipment along with a technical solution that allows the cooperation between the robotic vectors. To this end the paper presents architectural solutions for realizing the multi-agent monitoring platform as well as analyzes different possible scenarios for cooperation between aerial and surface water vectors.