Treatment for VATER involves surgery for each separate feature. Holes in the heart can be closed by surgery. Structural problems of the heart can also often be repaired. Prognosis is best for infants with small or simple heart problems. Some vertebral problems may also need surgery. If the vertebral differences cause a problem for the individual's posture, braces or other support devices may be needed.

Problems with the trachea and esophagus can also be repaired with surgery. Before surgery the infant usually needs a feeding tube for eating. This will stop the choking and spitting up. The infant may also need oxygen to help with breathing. If the trachea and esophagus are connected, the connection is separated first. Once separated, the two trachea ends and esophagus ends can be sealed together. When part of the esophagus is missing, the two loose ends are connected. If the gap between the loose ends is too big, surgery may be delayed until the esophagus grows. Some infants still have problems after surgery. They may have a difficult time swallowing or food may get stuck in their throat. They may also have asthma and frequent respiratory infections.

Surgery can also repair problems of the anus and rectum. Before surgery, a temporary opening is made from the small intestine to the abdomen. This allows the infant to have bowel movements and pass stool material. An anal opening is created with surgery. The intestines and rectum are adjusted to fit with the new anal opening. The temporary opening on the abdomen may be closed immediately after surgery or it may be closed weeks or months later. Surgeons must be very careful not to damage the nerves and muscles around the anus. If they are damaged, the individual may lose control of their bowel movements.

Differences of the hands and arms can also be improved with surgery. Infants with underdeveloped or absent radius may have a stiff elbow, stiff wrist, or twisted arm. Surgery can loosen the elbow and wrist to allow for movement. The arm can also be straightened. If needed, muscles from other parts of the body can be put into the arm. This may also improve movement. Even after surgery, individuals may not have completely normal function of the muscles and tendons of the arms and hands.