Bridge scour remains one of the leading causes of bridge failure globally, yet it is critically under-studied in sub-Saharan river systems, particularly in the complex hydrological environment of South Sudan's Nile tributary network. This study presents a comprehensive assessment of local and contraction scour phenomena at five representative bridge sites located on primary Nile tributaries — the Sobat, Bahr el Ghazal, Pibor, Kangen, and Akobo rivers — during the extreme wet season events of 2019–2023. Hydrological data, field measurements, and numerical modelling were integrated to estimate maximum scour depths using the HEC-18 framework, modified Richardson-Davis equations, and a newly proposed South Sudan Scour Index (SSSI). The results indicate that scour depths during peak flood events ranged from 1.8 m to 6.3 m across bridge types, with masonry arch and Bailey bridges exhibiting the highest vulnerability. Statistical correlation analysis revealed that peak discharge velocity (r = 0.89, p < 0.01) and sediment median grain size (D50) are the dominant predictive variables. A regional scour prediction model calibrated to Nile tributary hydraulics is proposed, offering a practical design tool for bridge engineers operating in tropical African river environments. Recommendations for scour countermeasures, real-time monitoring, and adaptive bridge design standards under extreme climate scenarios are provided.