Deterioration of road structural integrity because of flooding may cause huge expenditure for rehabilitation and maintenance of roadway. In principle, the design of pavement structure is based on the strength of compacted soil known as the subgrade or road foundation. Therefore, subgrade is a significant part of the road structural system. When roads are inundated for a long time or repeatedly, the materials in each layer of road structure become saturated, and the original condition of subgrade soils will be compromised. This study investigated the effect on sub-grade strength and properties due to road submergence period and repeated submergence of the road structural systems. Two types of soil that are normally used as the embankment material in road construction, which can be categorized as cohesive and cohesionless materials, were used in this study. California Bearing Ratio (CBR) test and consolidation settlement test were carried out on various categories of inundation and loading conditions including repeated inundation. The findings indicated that the strength of subgrade soil further decrease when they are inundated for a longer period. Similarly, consolidation test also shows that a quick and higher settlement could occur when the soil is inundated for a longer period. These findings are useful for road design and maintenance strategies of flood affected road links.