Abstract – Freshwater ecosystems are vast areas that are constantly changing and evolving. To maintain the ecosystem as well as the structures located close to bodies of water, frequent monitoring is required. Although dangerous and time consuming, manual operations are the conventional way of monitoring such areas. Recently, Autonomous Surface Vehicles (ASVs) have been proposed to undertake the monitoring task. As any other platform, ASVs have limitations, such as a restricted point of view and access only where the water is sufficiently deep. Unmanned Aerial Vehicles (UAVs) can fly over any terrain and provide a “bird’s‐eye‐view” of the environment. However, UAVs have limited operational time due to power constraints. Heterogeneous marsupial robotic systems use different types of robots to augment their operation envelope, taking advantage of their individual strengths. A marsupial survey system comprised an ASV and a UAV for freshwater monitoring is developed and presented in this paper. This system is able to complete long missions and reach remote locations while also being able to generate detailed maps and inspections of points of interest. The system was thoroughly tested during a 6‐month period in a number of field deployments in freshwater ecosystems at Lake Murray and at the Congaree River, SC, USA, to validate its capabilities.