The hemodynamic energy loss through the surgically implanted conduits determines the postoperative cardiac output and exercise capacity following the palliative repair of single-ventricle congenital heart defects. In this study, the hemodynamics of severely deformed surgical pathways due to torsional deformation and anastomosis offset are investigated. We designed a mock-up total cavopulmonary connection (TCPC) circuit to replicate the mechanically failed inferior vena cava (IVC) anastomosis morphologies under physiological venous pressure (9, 12, 15 mmHg), in vitro, employing the commonly used conduit materials: Polytetrafluoroethylene (PTFE), Dacron, and porcine pericardium. The sensitivity of hemodynamic performance to torsional deformation for three different twist angles (0 deg, 30 deg, and 60 deg) and three different caval offsets (0 diameter (D), 0.5D, and 1D) are digitized in three dimensions and employed in computational fluid dynamic (CFD) simulations to determine the corresponding hydrodynamic efficiency levels. A total of 81 deformed conduit configurations are analyzed; the pressure drop values increased from 80 to 1070% with respect to the ideal uniform diameter IVC conduit flow. The investigated surgical materials resulted in significant variations in terms of flow separation and energy loss. For example, the porcine pericardium resulted in a pressure drop that was eight times greater than the Dacron conduit. Likewise, PTFE conduit resulted in a pressure drop that was three times greater than the Dacron conduit under the same venous pressure loading. If anastomosis twist and/or caval offset cannot be avoided intraoperatively due to the anatomy of the patient, alternative conduit materials with high structural stiffness and less influence on hemodynamics can be considered.