Many remote communities lack access to reliable clean water and electricity, leading to the development of renewable powered desalination systems. To reduce costs of energy storage, many of these systems operate intermittently. However, the impact of intermittent operation on membrane fouling is still not well understood. This article presents an experimental investigation of the effect intermittent operation characteristic of renewable powered desalination systems has on membrane performance. Three operating conditions were investigated: use of anti-scalant or no anti-scalant; intermittent or continuous operation; and rinsing with 8 L of lab-grade clean water prior to shut-down or no rinsing. The results show intermittent operation increases the rate of membrane scaling. However, maintenance with rinsing prior to shut-down maintains higher membrane permeability than without rinsing. Membrane autopsy using scanning electron microscopy showed the fewest scale deposits for intermittent operation with anti-scalant and rinsing. On the sixth day of operation, the average normalized permeability declined to 87 +/- 9% for intermittent operation with anti-scalant and with rinse. All other operating conditions declined to nearly zero with the exception of continuous operation with anti-scalant, which declined to 30 +/- 4%. These experimental results will be used in future work to develop robust design algorithms for renewable powered desalination systems.