Expansive black cotton soils, classified as Vertisols in the FAO-UNESCO soil taxonomy and characterised by montmorillonite-dominated clay mineralogy, present exceptional geotechnical engineering challenges to bridge foundation design across the seasonally flooded plains of Warrap State, South Sudan. These soils undergo volumetric changes of 20–35% between wet and dry seasons, generating swell pressures that can exceed 300 kPa under saturated conditions and threaten the structural integrity of both shallow and deep foundation systems through heave-induced differential settlement, pile skin friction degradation, and horizontal pressures on abutment walls. This study presents the first systematic bearing capacity assessment of bridge foundations at six crossing sites on the Jur River and its principal tributaries in Warrap State, integrating comprehensive field investigations, laboratory geotechnical characterisation, analytical bearing capacity modelling, and finite element validation using PLAXIS 3D v23.1. Field investigations comprised Standard Penetration Tests at 1.5 m intervals, Consolidated Undrained triaxial testing, oedometer-based swell pressure measurements, X-ray diffraction mineralogical analysis, and in-situ vane shear tests at all six sites. Saturated undrained shear strengths range from 18 to 47 kPa, with oedometer-measured swell pressures of 85–312 kPa. Modified Terzaghi–Meyerhof bearing capacity equations incorporating swell pressure correction factors demonstrate that swell pressure eliminates effective bearing capacity for shallow foundations at four of six sites. PLAXIS 3D HSsmall finite element analysis validates analytical predictions within ±12%, confirming predicted maximum differential settlements of 12–34 mm and seasonal pile heave of 4–28 mm und