Non-targeted screening (NTS) in mass spectrometry (MS) helps alleviate the shortcoming of targeted analysis such as missing the presence of concerning compounds that are not monitored and its lack of retrospective analysis to subsequently look for new contaminants. Most NTS workflows include high resolution tandem mass spectrometry (HRMS2) and structure annotation with libraries which are still limited. However, in silico combinatorial fragmentation tools that simulate MS2 spectra are available to help close the gap of missing compounds in empirical libraries. Three NTS tools were combined and used to detect and identify unknown contaminants at ultra-trace levels in surface waters in real samples in this qualitative study. Two of them were based on combinatorial fragmentation databases, MetFrag and the Similar Partition Searching algorithm (SPS), and the third, the Global Natural Products Social Networking (GNPS), was an ensemble of empirical databases. The three NTS tools were applied to the analysis of real samples from a local river. A total of 253 contaminants were identified by combining all three tools: 209 were assigned a probable structure and 44 were confirmed using reference standards. The two major classes of contaminants observed were pharmaceuticals and consumer product additives. Among the confirmed compounds, octylphenol ethoxylates, denatonium, irbesartan and telmisartan are reported for the first time in surface waters in Canada. The workflow presented in this work uses three highly complementary NTS tools and it is a powerful approach to help identify and strategically select contaminants and their transformation products for subsequent targeted analysis and uncover new trends in surface water contamination.