Recent natural disasters that seriously affected critical infrastructure (CI) with significant socio-economic losses and impact revealed the need for the development of reliable methodologies for vulnerability and risk assessment. In this paper, a risk-based multi-level stress test method that has been recently proposed, aimed at enhancing procedures for evaluation of the risk of critical non-nuclear infrastructure systems against natural hazards, is specified and applied to six key representative CIs in Europe, exposed to variant hazards. The following CIs are considered: an oil refinery and petrochemical plant in Milazzo, Italy, a conceptual alpine earth-fill dam in Switzerland, the Baku–Tbilisi–Ceyhan pipeline in Turkey, part of the Gasunie national gas storage and distribution network in the Netherlands, the port infrastructure of Thessaloniki, Greece, and an industrial district in the region of Tuscany, Italy. The six case studies are presented following the workflow of the stress test framework comprised of four phases: pre-assessment phase, assessment phase, decision phase and report phase. First, the goals, the method, the time frame and the appropriate stress test level to apply are defined. Then, the stress test is performed at component and system levels and the outcomes are checked and compared to risk acceptance criteria. A stress test grade is assigned, and the global outcome is determined by employing a grading system. Finally, critical components and events and risk mitigation strategies are formulated and reported to stakeholders and authorities.