In the past 20 years, more than ten highways are built in the Lianyungang region, Jiangsu province, China. Among them, two highways (Coastal Highway A, close to the coastline, and Lianyan Highway B, approximately 25 km from the coastline) are crucial to the local highway network. However, the settlements of these two highways are significantly different, despite the same building method and location in a region with similar sediment provenance and sedimentary environment. A higher settlement rate was observed for the highway constructed far from the coastline. To clarify the mechanism, a series of field and laboratory tests based on regional geological survey were conducted in this study. Test results showed that the sensitivity difference of the soil induced by the pore water salinity leaching is the main reason for those observations. With pore water salinity leaching, the water content and plastic limit of Lianyungang marine soft clays remained almost unchanged, whereas the liquid limit and plasticity index of the soft clay near highway B gradually decreased with an increase in the liquidity index. The increase in the liquidity index subsequently decreased the remoulded strength of the soils far from the coastline. Simultaneously, the natural strength remained approximately the same due to leaching, and this led to an increase in the sensitivity, suggesting a strong structure. During the filling construction, the construction load and deviatoric stress under the embankment may have destroyed the clay structure. Therefore, a large settlement and high settlement rate resulted for the highway constructed far from the coastline.