Complex congenital heart disease (CHD) is associated with significant morbidity worldwide. Managing hypoxemia in these populations can be difficult, particularly in the setting of cyanotic CHD. However, the presence of additional extracardiac shunts secondary to acute respiratory disease can be very challenging to manage. Before understanding how to deal with hypoxemia in patients with dual shunts, one needs to understand the physiology and diagnosis related to the individual shunts and apply this knowledge to the patient as a whole.