Energy management is required to enable autonomous photovoltaic-powered membrane (PV-membrane) desalination systems to make the optimal use of solar energy. In this paper, a novel charge controller based on pre-set voltage sensing thresholds was designed to optimise the energy from PV panels and supercapacitors (SCs). The control algorithms were established from the data derivations with high-temporal-resolution (Is) solar irradiance (SI) source, allowing for resilient system operation under variable conditions. The impacts of ramp rates, in both SI and PV output voltage (V-PV) on the system, were systematically investigated. Under a worst-case scenario, with a rapid ramp rate of Delta V-PV = 2 V/s, the charge controller enabled the SCs to bridge the power gap to 6 min 20 s, permitting an additional 10 L of permeate water produced. The state-of-charge of the SCs varied from 11 to 86%, regardless of the magnitude of the ramp rate. The combination of the voltage thresholds (V-pump_on = 160 V and V-pump_off = 90 V) was determined to result in optimum system performance, realising a high permeate production at low specific energy consumption. It is concluded that the proposed charge controller is an effective method to enhance system resilience under worst-case solar conditions. (C) 2020 Elsevier Ltd. All rights reserved.