Fluctuations in solar irradiance were varied in frequency and magnitude to investigate the performance of a directly-connected solar energy powered reverse osmosis (RO) membrane system. Typically, the system produced acceptable quality water with constant solar irradiances ranging from 400 to 1200 W/ m2. Low average motor powers were encountered during fluctuations, however, in many cases, good performance was still realised, even at solar irradiance values that were equivalent to <400 W/m2. This counter-intuitive result arises from the effect of averaging the motor power, with periods of high solar irradiance compensating for the under-performance at times when the system was off. Overall, even though the permeate flux was often low when operating under fluctuating conditions, the RO system continued to deliver satisfactory quality water and at a low specific energy consumption (SEC). Temporal studies revealed that a disruption of the concentration polarisation layer occurs via a naturally induced backwash for steps in the solar irradiance as low as 100 W/ m2. This suggests that a renewable energy powered RO filtration system could benefit from being operated from a fluctuating energy source. Furthermore, the operating conditions during the first couple of minutes after a system shutdown event is shown to be very important, with: (i) shorter off-periods resulting in good performance being achieved quicker, and (ii) short-term power availability dramatically improving system performance. These findings indicate that a renewable energy powered RO system can operate well from a fluctuating energy source, in particular when additional power – for example, via supercapacitor energy buffering – is available to boost the system after a shut-down period.