Magnetic Resonance Imaging (MRI) velocimetry was applied to study non-invasively the water flow field inside a spiral-wound desalination membrane module (diameter: 2.5 in.; length: 18.5 in.), located in a pressure vessel, at typical practice operational conditions as a function of alginate fouling, simulating extracellular polymeric substances (EPS). Cross-sectional velocity images were acquired at an in-plane spatial resolution of 0.137 mm at multiple locations along the length of the reverse osmosis module and were acquired as a function of alginate concentration. At a total system alginate concentration of 3.25 mg/l, significant changes in the cross-sectional velocity map were observed near the module inlet due to alginate fouling, with limited changes observed in the middle and outlet regions of the module. When the total system alginate concentration was increased to 75 mg/l, it caused the module brine seal to fail resulting in significant local water flow by-passing the membrane module. This was clearly discernible in this opaque membrane system using MRI and resulting in dramatic changes in fluid velocity distribution through the membrane module. These observations of significant flow field heterogeneity as fouling develops are consistent with ‘irreversible’ fouling effects noted frequently in practice by the water treatment industry.