Supraglacial streams are a significant part of the glacial hydrological system and important for understanding the connection between glacial hydrology and glacier dynamics. Here we determine the factors that influence the development of step-pool formation and pulsating flow in a supraglacial stream on Bylot Island, Nunavut. Results show that during the second week of a 2-week study, multiple successive rainfall events occurred, stream temperature increased and ablation decreased; which also caused stream discharge to decrease. In addition, the stream, which flowed over a 13 m high waterfall off the front of Fountain Glacier, rapidly formed 21 step-pools and began to pulsate. The pulsating phenomenon involved the complete stoppage of flow over the waterfall and the subsequent restart between 8 and 20 s later. Pulsating flow resulted from rapid changes in the streambed morphology. In particular, the formation of the step-pool sequence was caused by helical flow around meander bends and hydrologically induced slippage along transverse shear planes, evidenced by observations of high-pressure artesian flow from transverse fractures. Contrary to previous literature, this study shows that high discharge is not necessarily the cause of step-pool formation and pulsating flow within supraglacial streams.