Integration of renewable energy and membrane filtration technologies such as nanofiltration (NF) and reverse osmosis (RO) can provide drinking water in places where freshwater is scarce and grid electrical connections are unavailable. This study investigated a directly-connected photovoltaic-powered membrane system under fluctuating solar conditions. Specifically, two configurations of NF/RO membranes with the same membrane area were investigated: a) 1 x 4 '' module, which contained one 4 '' NF/RO element; and b) 3 x 2.5 '' module, which contained three 2.5 '' NF/RO elements in series. A high fluoride brackish water ([F-] = 56.2 mg/L, total dissolved solids [TDS] = 4076 mg/L) collected from northern Tanzania was treated by different membranes in the two configurations. Performance indicators such as flux, specific energy consumption, and permeate F- concentration were monitored over a 60-min period of energy fluctuation that are part of a typical solar day. The results showed that the overall performance of the 1 x 4 '' module was superior to that of the 3 x 2.5 '' module. This is because the performance of a 3 x 2.5 '' module degraded significantly from the first element to the third element due to the increased feed concentration and the decreased net driving pressure. Three 1 x 4 '' modules (BW30, BW3OLE and NF90) and one 3 x 2.5 '' module (BW30) were able to meet the drinking water guideline for fluoride. During cloud periods, the transient permeate F- concentration exceeded the guideline value due to insufficient power, however the cumulative permeate F- concentration was always well below the guideline. The photovoltaic-powered membrane system equipped with the above modules provides a promising solution for addressing drinking water problems in remote and rural areas.