Abstract On-line continuous monitoring of water bodies produces large quantities of high frequency data. Long-term quality control and applicability of these data require rigorous storage and documentation. To carry out these activities successfully, a database has to be built. Such a database should provide the simplicity to store and document all relevant data and should be easy to use for further data evaluation and interpretation. In this paper, a comprehensive database structure for water quality data is proposed. Its goal is to centralize the data, standardize their format, provide easy access, and, especially, document all relevant information (metadata) associated with the measurements in an efficient way. The emphasis on data documentation enables the provision of detailed information not only on the history of the measurements (e.g., where, how, when and by whom was the value measured) but also on the history of the equipment (e.g., sensor maintenance, calibration/validation history), personnel (e.g., experience), projects, sampling sites, etc. As such, the proposed database structure provides a robust and efficient tool for functional data storage and access, allowing future use of data collected at great expense.