A system and method for using a pulse flow to circulate algae in an algae cultivation apparatus are provided. In order to counteract the negative effects of biofouling on algae cultivation equipment, a pulse flow is created to periodically move through an algae cultivation apparatus. The pulse flow will dislodge algae cells adhering to various surfaces of the apparatus, and it will also create turbulence to stir up any algae cells which may have settled onto the bottom of the apparatus. To produce an increased fluid flow rate required to create an effective pulse flow, a sump, which is periodically filled with drawn algal culture from the apparatus, is located at an elevated position above the apparatus. When released, the algal culture travels through a transfer pipe and into the apparatus with gravity causing the algal culture to flow at a very high rate.