Flooding may affect chemical facilities leading to major accidents (fires, explosions, contamination), following damages to structures and equipment. This type of accident is indicated as natural-technological (Natech) event and occurred in the past, often leading to severe accidental scenarios. Recent studies allowed developing a specific methodology aimed at including Natech scenarios triggered by flooding into Quantitative Risk Assessment (QRA) analyses for chemical facilities. The methodology relies on the use of specific fragility models for the evaluation of failure probability of process units affected by flooding. Despite these models consider different types of equipment geometries and flooding conditions, they do not account for the presence of safety barriers (e.g., fire-protection systems, bunds, blanketing system). In the present work, the previously developed QRA methodology is improved in order to provide a risk-based vulnerability analysis of Natech scenarios induced by severe flooding taking into account the presence of safety barriers. The methodology is improved by including the availability assessment of safety barriers based on the possibility the systems have been impacted by the flood. A tailored Failure Mode and Effect and Criticality Analysis (FMECA) is presented for assessing the damages to safety barriers resulting from flooding events. As an example, the analysis of an important safety barrier through the FMECA approach is presented. The study shows an example of both risk informed decision-making concerning protection systems and development of new criteria for the assessment of safety barrier failure in case of natural hazards.