This study presents a new multi-index hierarchical model for flood risk assessment which incorporates three indicator indexes—hazard, vulnerability, and exposure—to develop a five-level risk scale. The methodology is applied to historical data on flood events in The Slovak Republic between 2001 and 2010. The input values are characterized in more detail through the use of weighted values to provide a more balanced overall risk assessment. The original formula used to calculate the risk levels was found to produce results with overly high numerical values, and therefore the multiplication step of the formula was replaced by addition to insure greater simplicity and ease of use. This refined methodology introduces a novel quantitative approach to risk assessment, offering flexibility and variability in the indicator layer. The methodology can be adapted to assess risk at either the macro or micro scale and at more specific periods of time. The resulting risk values offer a nuanced understanding of risk levels across different indexes and underscores the method’s innovation.