Congenital heart disease associated with situs ambiguus is frequently characterized by complex and heterogeneous abnormalities of systemic and pulmonary venous return. These anomalies are associated with atrioventricular septal defects and interrupted inferior vena cava, particularly in the setting of heterotaxy syndromes. We report a 2-year-old male child (10.5 kg) with complex congenital heart disease and inconsistent findings across multiple echocardiographic studies. Initial assessments suggested atrioventricular septal defect with variable ventricular balance and systemic venous anomalies. Cardiac CT demonstrated situs ambiguus, levocardia, common atrioventricular canal features, anomalous hepatic venous drainage into the left atrium, and partial anomalous pulmonary venous drainage, and absent of left SVC. Intraoperatively, more complex anatomy was identified, including two large atrial septal defects or common atrium without ventricular septal defect, cleft mitral valve, left superior vena cava draining into the left atrium, interrupted inferior vena cava with hepatic venous drainage into the left atrium, and partial anomalous pulmonary venous return to the right atrium. Surgical repair included atrioventricular valve repair, baffling of left superior vena cava and hepatic venous drainage using bovine pericardium, closure of atrial septal defects. Tricuspid and mitral valve repair and finally removal of pulmonary artery band and augmentation of main pulmonary artery with bovine pericardium. The postoperative course was complicated by arrhythmias requiring temporary pacing, low cardiac output syndrome, and need for peritoneal dialysis, followed by full recovery and discharge after 10 days to home. This case highlights rare combination of systemic and pulmonary venous anomalies associated with atrioventricular septal defects and interrupted inferior vena cava which illustrate the limitations of echocardiography and CT in complex systemic and pulmonary venous anomalies with heterotaxy syndromes and underscores the importance of intraoperative assessment.