Renewable energy powered membrane systems operate with fluctuating energy. Such fluctuations affect pressure and feed flow and as such the hydrodynamic conditions in a membrane system. Hydrodynamic variations alter the membrane surface concentration and boundary layer thickness which in turn determines permeate water quality. In this work this is calculated using computational fluid dynamics (CFD) for the three most predominant energy levels obtained during such fluctuations and compared with experimental data.A 2D-CFD simulation was performed using OpenFOAM to calculate the wall concentration and boundary layer thickness over the length of a module. The influence of module type was investigated using two system configurations, namely three 2.5″ modules in series (BW30-2540 or NF270-2540) and one 4″ module (BW30-4040 and NF270-4040) with similar total membrane areas. Energy levels were extracted from experimental data at three solar irradiance, maximum intensity (1 kW/m2), light cloud (360 W/m2) and heavy cloud periods (190 W/m2).At the highest energy level, in the system with three 2.5″ modules the wall concentration was closer to the bulk concentration due to the higher flow velocity in a smaller channel. The resulting boundary layer thickness for BW30 was constant and almost zero. At the medium energy level, the simulation results show that the permeate flux decreased significantly due to the lower pressure and for the BW30 it was almost zero due to the low pressure. At the lowest energy level, the feed pressure was well below the osmotic pressure and no permeation was possible.Results from this study show that the model is able to describe the filtration process in spiral wound membrane modules under fluctuating energy conditions. Further investigations on the possibility to improve the boundary conditions of the model are required.