Pollution in the Port of Gdynia can encompass various types of substances and contaminants that affect the quality of water and sediment in this region. Ships entering and leaving the port can release pollutants such as oil, fuel, waste, and chemicals into the water. Controlling and monitoring these pollutants is a crucial part of environmental stewardship. In recent years, uncrewed units have been increasingly in use for in situ water and sediment sampling. Boat-based water sampling crews face significant safety risks at sea. Eliminating the need for a boat-based sampling crew, uncrewed units allow sampling from locations that are difficult to access by traditional sampling methods. To validate the HydroDron-1 method, water samples and bottom sediments were collected from five basins in the Port of Gdynia using the HydroDron-1 method and accredited sampling methods. The values of measured parameters were similar for both methods. Using the HydroDron-1 method at the Port of Gdynia has the potential to improve safety while reducing sampling costs and increasing data collection. The project was implemented as part of the POLNOR 2019 Call program, announced by the National Center for Research and Development (NCRD): “Marine port surveillance and observation system using mobile unmanned research units” NOR/POLNOR/MPSS/0037/2019.