Water is essential for life and the protection of this vital resource is paramount to ensuring quality of life. Millions of chemicals are produced annually and these chemicals, the reactants, by-products and/or transformation products end up at some stage in the water cycle, in potentially toxicologically relevant concentrations. As many of these chemicals remain unidentified, the risk posed to the environment and human health cannot be fully assessed. Current strategies for water monitoring only include a very limited selection of “priority pollutants”, which is insufficient for public and environmental protection. This project aims to improve the identification of unknown chemicals in water samples, using cutting edge analysis techniques (LC-LTQ-Orbitrap-MS(n)) and automated data-processing strategies for compounds detected in any given water sample. Current strategies involving database searching will be explored and optimised to create a user-friendly workflow to streamline identification efforts for routine monitoring applications, where time is the essence. As database searching does not deliver the right answer in many cases, the development of identification strategies based on structure generation will also be a major focus of this work. In this case, all possible molecules are considered, not just those in the database, resulting in a far more complicated workflow. The structure generation strategy will incorporate the latest identification procedures within the environmental and metabolomics fields and will benefit from collaborations with several leading partners in these fields. The outcomes of this study will be applicable not only to environmental and metabolomics approaches but also for pharmaceutical, forensic and medicinal applications.