Emerging Pollutants (EPs) are synthetic organic compounds identified in the environment that may potentially threaten ecological systems and human health. They can enter water systems from a variety of sources and are of particular concern due to their potential for bioaccumulation and toxicological effects. Their origin and environmental impact are not yet fully understood, so the monitoring of these compounds by regulatory bodies is not yet completely established. EPs cover a broad spectrum of substances, including pharmaceuticals, personal care products, endocrine disruptors, pesticides, and microplastics, that are not always detected by traditional monitoring targeted analysis. Non-targeted analysis (NTA) or suspect screening (SS) employing high-resolution mass spectrometry has emerged as a promising tool for environmental monitoring to identify and prioritize a broader spectrum of emerging contaminants that are not routinely monitored and their transformation products. Here we present a comprehensive review of NTA strategies for screening EPs, covering major insights on the current methodologies and limitations, workflows used for NTA and considerations during sampling, sample preparation, instrumental data acquisition, analysis, and approaches for identification and prioritization of EP in water sources. We have ultimately prioritized predominant and toxic compounds in groundwater, drinking water, surface water, wastewater, and leachates.