Flexible pavement structures are vulnerable due to the degradation of unbound materials after water inundation. This study aims to evaluate the resilience of flexible pavements to flooding events using an integrated hydraulic and mechanical modeling approach. Two-dimensional hydraulic models were established to analyze flooding-induced moisture variations in the pavements. Based on the moisture variation results, three-dimensional mechanical models that considered the moisture-stress-matric suction-dependent modulus of unbound materials were developed to calculate critical pavement responses under vehicular loading. The increases in critical pavement responses due to flooding were analyzed and the increase in pavement damage during post-flooding recovery processes was predicted. The proposed methodology provides an effective way of quantifying the impact of flooding on long-term pavement performance.