In Potter syndrome, the primary problem is kidney failure. The kidneys fail to develop properly as the baby is growing in the womb. The kidneys normally produce the amniotic fluid (as urine).

Potter phenotype refers to a typical facial appearance that occurs in a newborn when there is no amniotic fluid. The lack of amniotic fluid is called oligohydramnios. Without amniotic fluid, the infant is not cushioned from the walls of the uterus. The pressure of the uterine wall leads to an unusual facial appearance, including widely separated eyes .

Potter phenotype may also lead to abnormal limbs, or limbs that are held in abnormal positions or contractures.

Oligohydramnios also stops development of the lungs, so the lungs do not work properly at birth.