Transportation infrastructure needs significant financial costs, and due to growing traffic volume and changing weather, it is prone to degradation and failure. The National Highway Authority of India started construction of the Thalassery–Mahe bypass in October 2018, and it was nearing completion in March 2023. Between Dharmadam bridge and Balam underpass, the area was waterlogged, and geotechnical investigation shows the top 15 m of very soft clay. Ground improvement with timber pile over which composite layers of geocells/geotextiles were provided for embankment foundation. Retaining walls were constructed on both sides, and filling of the embankment was planned up to 8.50 m. When embankment work reached a height of 6.50 m, failure in the foundation system was noted due to bearing capacity failure with cracks in the retaining wall and embankment. The upheaval of soils in the water-logged area outside the retaining wall was noted. Forensic investigation studies showed inadequate improvement of the strength of clay and stresses induced are much higher than in design. To counter-surcharge loads, it was suggested to provide balancing berms outside the RC walls. Numerical modelling of the embankment system was carried out for optimum balancing berm design. Since failure had happened and the compacted fill of 6.50 m was completed, it was difficult and time-consuming to adopt new ground improvement techniques to improve the soft clay deposit beneath after removing the fill. Instead of further filling, bored cast in situ DMC Piles terminating with adequate anchorage into the hard rock were adopted with structural girder and slab till embankment height is within 2 m to complete the project in the scheduled time.