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This paper presents the development and implementation of a sensor network based on the Internet of Things (IoT) for monitoring key groundwater quality parameters to minimize potential risks in biodiversity conservation. These water monitoring parameters include the water level, water temperature, pH, conductivity, and dissolved oxygen (DO). The system ensures scalability, ease of use, real-time data acquisition and minimal power consumption resulting in efficient and reliable water quality monitoring with the convenience of remote sensing. The continuous measurement system was set up to be a single source of information for monitoring groundwater quality in protected wetland areas across international borders, including Tompojevacki Ritovi (Municipality of Tompojevci, Croatia) and Lake Zobnatica (Municipality of Backa Topola, Serbia). The data collected over one year and three months by the wireless sensor network (WSN) monitoring were compared to standard laboratory method results to demonstrate the accuracy and precision of the WSN measurements. The relative mean (average) error for the WSN measurements compared with the laboratory analyses results have the following values: 8.8% for pH, 10.3% for DO, 33.7% for conductivity on sites in Tompojevci; 4.6% for pH, 12.8% for DO, 29.5% for conductivity on sites in Lake Zobnatica. Appropriate calibration and installation of the WSN give a larger volume of data and thus grow the database, allowing for a more accurate identification of water contamination and a quick response in the event of pollution. Smart IoT-based sensors help to protect water quality and, as a result, the well-being of ecosystems and human communities, which is especially important in protected areas like wetlands. © 2024 IOP Publishing Ltd. All rights, including for text and data mining, AI training, and similar technologies, are reserved.