Around 30–40 years ago, principles and methods were developed to conceptualise, assess and manage risk. These principles and methods are still, to a large extent, the foundation of the field. Over the past decade, many tools have been developed for risk analysis of water systems. Many advances have been made, both in the theoretical platform and in practical models and procedures. Various risk analysis approaches have been used to identify potential hazards, calculate the probability of accidents and assess the severity of consequences. The objective of this paper is to review these developments, focusing on the fundamental ideas and thinking behind them, considering their application at strategic, programmatic and operational levels of decision-making, in order to improve the understanding of stakeholders (researchers, regulators, etc.). To achieve this objective, scientific papers on risk analysis associated with water treatment systems were identified and reviewed, with particular focus on risk assessment methods (qualitative, semi-qualitative or quantitative, deterministic or probabilistic, etc.), tools (ETA, FTA, FMEA/FMECA, QMRA, HRA, Markov, etc.), applicability of these tools and results of case studies. A total of 141 references were selected on the basis of title sorting from databases as ScienceDirect, PubMed, Scopus, ISI Web of Science or SpringerLink, and a total of 68 articles were selected for full-text analysis. Main conclusions of this review and analysis efforts are as follows: (1) the scientific foundation of risk assessment and risk management is still an open issue; (2) principles, theories and base methods applicable to water supply systems are in continuous development, existing tools are suitable, and a growing number of applications are available and of great interest; and (3) risk analysis methodologies are in their journey to gain the necessary broad technical, community and political acceptance in the water treatment sector, and some gaps and opportunities have been included in the discussion.